Reduction of off-target rna interference toxicity

ABSTRACT

The present invention is directed to RNA interference (RNAi) molecules targeted against a nucleic acid sequence, and methods of using these RNAi molecules to reduce off-target toxicity.

PRIORITY OF INVENTION

The present patent application is a continuation-in-part application ofU.S. application Ser. No. 12/111,025 filed on Apr. 28, 2008, whichclaims priority under 35 U.S.C. § 119(e) to U.S. Provisional ApplicationNo. 60/914,309 filed on Apr. 26, 2007. The present patent applicationalso claims priority under 35 U.S.C. § 119(e) to U.S. ProvisionalApplication No. 60/932,468 filed on May 31, 2007, to U.S. ProvisionalApplication No. 61/038,685 filed on Mar. 21, 2008, and to U.S.Provisional Application No. 61/070,622 filed on Mar. 25, 2008.

The present application claims the benefit of all of the above-listedapplications, which are hereby incorporated by reference herein in theirentireties, including the drawings.

GOVERNMENT SUPPORT

This invention was made with government support under NS-50210,HD044093, DK-54759 and NS-592372 awarded by the National Institutes ofHealth. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Double-stranded RNA (dsRNA) can induce sequence-specificposttranscriptional gene silencing in many organisms by a process knownas RNA interference (RNAi). However, in mammalian cells, dsRNA that is30 base pairs or longer can induce sequence-nonspecific responses thattrigger a shut-down of protein synthesis. Interference of geneexpression by RNAi molecules is now recognized as a naturally occurringstrategy for silencing genes in the cells of many organisms.

Cells can contain various small dsRNAs (˜21-25 bp). Two types of smallRNA molecules have a post-transcriptional effect: (1) siRNA moleculesthat induce mRNA degradation, and (2) miRNAs, also called microRNAs,that induce translational inhibition. Other small RNAs work at thetranscriptional level by affecting DNA and histone methylation. RNAimolecules can be generated exogenously (e.g., siRNA molecules), andinduce transient gene silencing. Alternatively, RNAi molecules can beintroduced via a vector that expresses short-hairpin RNAs (shRNA) inorder to exhibit persistent gene silencing.

SUMMARY OF THE INVENTION

The present invention provides an isolated miRNA shuttle vector thatexpresses a therapeutic siRNA with limited off target toxicity. Incertain embodiments, embedding an siRNA that exhibits off targettoxicity in the context of an shRNA shuttle vector within the miRNAshuttle vectors of the present invention limits the off target toxicityof the siRNA. In certain embodiments, the miRNA shuttle vector expressesa therapeutic siRNA in the brain with limited off target toxicity. Incertain embodiments, the miRNA shuttle vector expresses a therapeuticsiRNA in the striatum with limited off target toxicity. In certainembodiments, the miRNA shuttle vector expresses a therapeutic siRNA inthe cerebrum with limited off target toxicity.

The present invention provides an isolated nucleic acid encoding aprimary transcript (pri-miRNA) including, in order of position, a5′-flanking region, a first siRNA region, a loop region, a second siRNAregion, and a 3′-flanking region (FIG. 20A-20F). In certain embodiments,the 5′-flanking region is contiguously linked to the first siRNA region,the loop region is positioned between the first siRNA region and thesecond siRNA region, and the second siRNA region is contiguously linkedto the 3′-flanking region. In certain embodiments, the first siRNAregion is a non-guide region and the second siRNA region is a guideregion, and in other embodiments the first siRNA region is a guideregion and the second siRNA region is a non-guide region. As usedherein, the term “siRNA guide region” is a single-stranded sequence ofRNA that is complementary to a target sequence. As used herein, the term“siRNA non-guide region” is a single-stranded sequence of RNA that iscomplementary to the “siRNA guide region.” Thus, under the properconditions, the siRNA guide region and the siRNA non-guide regionassociate to form an RNA duplex. As used herein, all nucleic acidsequences are listed, as is customary, in a 5′ to 3′ direction.

In certain embodiments, the first siRNA region is about 20-30nucleotides in length, and is about 70-100% complementary to the secondsiRNA region, which is also about 20-30 nucleotides in length.

In certain embodiments, the 5′-flanking region contains a 5′-joiningsequence contiguously linked to the first siRNA region (FIGS. 20B and20C). As used herein, the term “joining site” or a “joining sequence” isa short nucleic acid sequence of less than 60 nucleotides that connectstwo other nucleic acid sequences. In certain embodiments, the joiningsite is of a length of any integer between 4 and 50, inclusive. Incertain embodiments, the 5′-joining sequence consists of 5-7 nucleotides(e.g., consists of 6 nucleotides). In certain embodiments, the5′-joining sequence encodes GUGASSS, wherein S is either a G or Cnucleotide (i.e., the 5′-joining sequence encodes UGACCC, UGACCG,UGACGC, UGAGCC, UGACGG, UGAGGC, UGAGCG, or UGAGGG). In certainembodiments, the 5′-joining sequence encodes GUGAGCG.

In certain embodiments, the 5′-flanking region further comprises a5′-bulge sequence positioned upstream from the 5′-joining sequence. Asused herein, the term “bulge sequence” is a region of nucleic acid thatis non-complementary to the nucleic acid opposite it in a duplex. Forexample, a duplex will contain a region of complementary nucleic acids,then a region of non-complementary nucleic acids, followed by a secondregion of complementary nucleic acids. The regions of complementarynucleic acids will bind to each other, whereas the centralnon-complementary region will not bind, thereby forming a “bulge.” Incertain embodiments the two strands of nucleic acid positioned betweenthe two complementary regions will be of different lengths, therebyforming a “bulge.” In certain embodiments, the 5′-bulge sequence willcontain from 2 to 15 nucleotides. In certain embodiments, the 5′-bulgesequence consists of about 1-10 nucleotides. In certain embodiments, the5′-bulge sequence encodes UAAACUCGA. In certain embodiments, the5′-bulge sequence has from 0-50% complementarity to the 3′-bulgesequence. The XhoI restriction site is CTCGAG (with “T” being “U” in RNAform in this and all other sequences listed herein).

In certain embodiments, the 5′-flanking region further contains a5′-spacer sequence positioned upstream from the 5′-bulge sequence. Incertain embodiments, the 5′-spacer sequence consists of 9-12nucleotides, such as 10-12 nucleotides. In certain embodiments, the5′-spacer sequence has from 60-100% complementarity to a 3′-spacersequence. In certain embodiments, the 5′-bulge sequence comprises acloning site, such as an XhoI site. In certain embodiments, the5′-spacer sequence is UGGUACCGUU (SEQ ID NO:180).

In certain embodiments, the 5′-flanking region further contains a5′-upstream sequence positioned upstream from the 5′-spacer sequence. Incertain embodiments, the 5′-upstream sequence is about 5-5000nucleotides in length, such as 30-2000 nucleotides in length.

In certain embodiments, the 3′-flanking region contains a 3′-joiningsequence contiguously linked to the second siRNA region (FIGS. 20D and20E). In certain embodiments, the joining site is of a length of anyinteger between 4 and 50, inclusive. In certain embodiments, the3′-joining sequence consists of 5-7 nucleotides, (e.g., consists of 6nucleotides). In certain embodiments, the 3′-joining sequence is atleast about 85% complementary to a 5′-joining sequence. In certainembodiments, the 3′-joining sequence encodes CGCYUAC, wherein Y is C orU. In certain embodiments, the 3′-joining sequence encodes CGCCUAC.

In certain embodiments, the 3′-flanking region further comprises a3′-bulge sequence positioned downstream from the 3′-joining sequence. Incertain embodiments, the 3′-bulge sequence comprises a cloning site,such as a SpeI/XbaI site or a SpeI site. The SpeI/XbaI site is encodedby CTCAGA, and the SpeI site is encoded by CTCAGT. In certainembodiments, the 3′-bulge sequence consists of about 1-15 nucleotides(such as 2-15 nucleotides or 1-10 nucleotides). In certain embodiments,the 3′-bulge sequence encodes UAG. In certain embodiments, the 5′-bulgesequence is complementary to the 3′-bulge sequence at only onenucleotide at each end of the sequence.

In certain embodiments, the 3′-flanking region further contains a3′-spacer sequence positioned downstream from the 3′-bulge sequence. Incertain embodiments, the 3′-spacer sequence consists of 9-12nucleotides, such as 10-12 nucleotides. In certain embodiments, the3′-spacer sequence is AGCGGCCGCCA (SEQ ID NO:181). In certainembodiments, the 3′-spacer sequence is at least about 70% complementaryto a 5′-spacer sequence.

In certain embodiments, the 3′-flanking region further contains a3′-downstream sequence positioned downstream from the 3′-spacersequence. In certain embodiments, a 5′-upstream sequence does notsignificantly pair with the 3′-downstream sequence. As used herein, theterm “does not significantly pair with” means that the two strands areless than 20% homologous. In certain embodiments, the 3′-downstreamsequence is about 5-5000 nucleotides in length, such as 30-2000nucleotides in length.

In certain embodiments, the loop region is from 4-20 nucleotides inlength, such as 15-19 nucleotides in length. From 0-50% of the loopregion can be complementary to another portion of the loop region. Asused herein, the term “loop region” is a sequence that joins twocomplementary strands of nucleic acid. In certain embodiments, 1-3nucleotides of the loop region are immediately contiguous to thecomplementary strands of nucleic acid may be complementary to the last1-3 nucleotides of the loop region. For example, the first two nucleicacids in the loop region may be complementary to the last twonucleotides of the loop region. In certain embodiments, the loop regionis 17 nucleotides in length. In certain embodiments, the loop regionencodes CUNNNNNNNNNNNNNNNGG (SEQ ID NO:182) or CCNNNNNNNNNNNNNNNGG (SEQID NO: 183). In certain embodiments, the loop region encodesCUGUGAAGCCACAGAUGGG (SEQ ID NO: 184) or CCGUGAAGCCACAGAUGGG (SEQ ID NO:185).

The present invention further provides an RNA encoded by nucleic aciddescribed herein.

The present invention further provides an expression cassette containinga promoter contiguously linked to the nucleic acid described herein. Incertain embodiments, the promoter is a polII or a polIII promoter, suchas a U6 promoter (e.g., a mouse U6 promoter). In certain embodiments,the expression cassette further contains a marker gene. In certainembodiments, the promoter is a polII promoter. In certain embodiments,the promoter is a tissue-specific promoter. In certain embodiments, thepromoter is an inducible promoter. In certain embodiments, the promoteris a polIII promoter.

The present invention provides a vector containing an expressioncassette described herein. In certain embodiments, the vector is anadeno-associated virus (AAV) vector.

The present invention provides a non-human animal comprising the nucleicacid, the expression cassette, or the vector described herein.

The present invention provides a composition that comprises shHD(2.1),shHD(2.1b), sh1913, shGFP, miSCA1, shSCA1, miJNK, miHTT, miHD2.4,miHD2.4.2, miHD8.2, miHD8.2.2, miHD8.2.3, miSCA1-2225 or miSCA1-1399.

The present invention provides an expression cassette encodingshHD(2.1), shHD(2.1b), sh1913, shGFP, miSCA1, shSCA1, miJNK, miHTT,miHD2.4, miHD2.4.2, miHD8.2, miHD8.2.2, miHD8.2.3, miSCA1-2225 ormiSCA1-1399. In certain embodiments, the expression cassette furthercontains a marker gene.

The present invention provides a vector comprising an expressioncassette encoding shHD(2.1), shHD(2.1b), sh1913, shGFP, miSCA1, shSCA1,miJNK, miHTT, miHD2.4, miHD2.4.2, miHD8.2, miHD8.2.2, miHD8.2.3,miSCA1-2225 or miSCA1-1399.

The present invention provides a non-human animal comprising shHD(2.1),shHD(2.1b), sh1913, shGFP, miSCA1, shSCA1, miJNK, miHTT, miHD2.4,miHD2.4.2, miHD8.2, miHD8.2.2, miHD8.2.3, miSCA1-2225 or miSCA1-1399, oran expression cassette or vector encoding these shRNAs or miRNAs.

The present invention provides method of inducing RNA interference byadministering to a subject a nucleic acid, an expression cassette, avector, or a composition described herein.

The present invention provides a vector containing a U6 promoteroperably linked to a nucleic acid encoding an miRNA. The predictedtranscription start sites of constructs of the present invention aredifferent from those used by researchers in the past. In certainembodiments of the present invention, the U6miRNA has an extended 5′end. If the 5′ end is truncated to resemble the previous CMV-basedstrategy, silencing efficacy is severely reduced. The present inventionalso provides improved flanking sequences that show improved efficacyover natural miR-30 flanking sequences. The use of the present miRNAstrategy appears to alleviate toxicity associated with traditional shRNAapproaches. The miRNA strategy does not generally generate excessiveamounts of RNAi as do U6shRNA approaches.

As used herein the term “stem sequence” is a sequence that iscomplementary to another sequence in the same molecule, where the twocomplementary strands anneal to form a duplex (e.g., the first andsecond siRNA regions). The duplex that is formed maybe fullycomplementary, or may be less than fully complementary, such as 99%,98%, 97%, 96%, 95,%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%,84%, 83%, 82%, 81%, 80%, 75%, or 70% complementary to each other.Further, in certain embodiments, one strand may contain more nucleotidesthan the other strand, allowing the formation of a side loop.

In certain embodiments, a first siRNA region consists of5′-AAAAGAACUUUCAGCUACCAAG-3′ (SEQ ID NO: 186) and the second siRNAregion consists of 5′-UUUGGUAGCUGAAAGUUCUUUC-3′ (SEQ ID NO:187) (seeFIG. 16, miHD(2.1)).

In certain embodiments, a first siRNA region consists of5′-CAGAAAGAACUUUCAGCUACCG-3′ (SEQ ID NO: 188) and a second siRNA regionconsists of 5′-UGGUAGCUGAAAGUUCUUUCUU-3′ (SEQ ID NO: 189) (see FIG. 16,miHD(2.1b)).

In certain embodiments, a first siRNA region consists of5′-CAGCCCAGGUCAGCGUUGAAGU-3′ (SEQ ID NO:190) and a second siRNA regionconsists of 5′-ACUUCAACGCUGACCUGGGCUU-3′ (SEQ ID NO:191) (see FIG. 16,mi1913).

In certain embodiments, a first siRNA region consists of5′-CAGCACAAGCUGGAGUACAAUU-3′ (SEQ ID NO: 192) and a second siRNA regionconsists of 5′-AGUUGUACUCCAGCUUGUGCUU-3′ (SEQ ID NO:193) (see FIG. 16,miGFP).

In certain embodiments, a first siRNA region consists of5′-CAGCACAAGCUGGAGUACAAUU-3′ (SEQ ID NO:194) and a second siRNA regionconsists of 5′-AGUUGUACUCCAGCUUGUGCUU-3′ (SEQ ID NO:195) (see FIG. 16,mi1913-miR30 variant).

In certain embodiments, a first siRNA region consists of5′-CGACCGUGUGAAUCAUUGUUUA-3′ (SEQ ID NO:196) and a second siRNA regionconsists of 5′-UAGACAAUGAUUCACACGGUCA-3′ (SEQ ID NO: 197) (see FIG. 19,miHD2.4).

In certain embodiments, a first siRNA region consists of5′-CACCGUGUGAAUCAUUGUCUAA-3′ (SEQ ID NO:198) and a second siRNA regionconsists of 5′-CAUUAGACAAUGAUUCACACGGUA-3′ (SEQ ID NO: 199) (see FIG.19, miHD2.4.2).

In certain embodiments, a first siRNA region consists of5′-CAGCAGCUUGUCCAGGUUUAUG-3′ (SEQ ID NO:200) and a second siRNA regionconsists of 5′-UAUAAACCUGGACAAGCUGCUA-3′ (SEQ ID NO:201) (see FIG. 19,miHD8.2).

In certain embodiments, a first siRNA region consists of5′-CAGAGCAGCUUGUCCAGGUUUA-3′ (SEQ ID NO:202) and a second siRNA regionconsists s of 5′-UAAACCUGGACAAGCUGCUCUA-3′ (SEQ ID NO:203) (see FIG. 19,miHD8.2.2).

In certain embodiments, a first siRNA region consists of5′-AAGAGCAGCUUGUCCAGGUUUA-3′ (SEQ ID NO:204) and a second siRNA regionconsists of 5′-UAAACCUGGACAAGCUGCUCUC-3′ (SEQ ID NO:205) (see FIG. 19,miHD8.2.3).

In certain embodiments, a first siRNA region consists of5′-CGGCGAACUGAAGUUUCCAGAA-3′ (SEQ ID NO:206) and a second siRNA regionconsists of 5′-UUCUGGAAACUUCAGUUCGCCA-3′ (SEQ ID NO:207) (see FIG. 19,miSCA1-2225).

In certain embodiments, a first siRNA region consists of5′-CGACCGUGUGAAUCAUUGUUUACCGGCCAGCAGCAAGCAAUCAU-3′ (SEQ ID NO:208) and asecond siRNA region consists of 5′-GUGAUUGCUUGCUGCUGGCCGA-3′ (SEQ IDNO:209) (see FIG. 19, miSCA1-1399).

In certain embodiments, the nucleic acid of the invention does notencode a sequence consisting of SEQ ID NO:219, SEQ ID NO:220, SEQ IDNO:221 or SEQ ID NO:222.

The present invention also provides vectors containing the expressioncassettes described herein. Examples of appropriate vectors includeadenoviral, lentiviral, adeno-associated viral (AAV), poliovirus, herpessimplex virus (HSV), or murine Maloney-based viral vectors. In oneembodiment, the vector is an adeno-associated virus vector. Thesecassettes and vectors may be contained in a cell, such as a mammaliancell. A non-human mammal may contain the cassette or vector.

The present invention provides cells (such as a mammalian cell)containing the nucleic acid molecules, expression cassettes or vectorsdescribed herein. The present invention also provides a non-human mammalcontaining the nucleic acid molecules, expression cassettes or vectorsdescribed herein.

The present invention provides a nucleic acid, an expression cassette, avector, or a composition as described herein for use in therapy, such asfor treating a neurodegenerative disease.

The present invention provides an isolated RNAi molecule having amicroRNA having an overhang at the 3′ end. In certain embodiments, theoverhang is a 2 to 5-nucleotide repeat. In certain embodiments, theoverhang is a UU, UUU, UUUU CUU, CUUU or CUUUU sequence. In certainembodiments, the microRNA is a naturally-occurring microRNA. In certainembodiments, microRNA is an artificial microRNA. In certain embodiments,the RNAi molecule produces a decreased level of off-target toxicity.

The present invention provides a method of inducing low-toxicity RNAinterference by administering to a subject a nucleic acid, an expressioncassette, a vector, or a composition as described herein. In certainembodiments, the expression cassette contains a polII promoter.

The present invention provides a method of inducing low-toxicity RNAinterference by administering to a subject an expression cassetteencoding a polII promoter operably linked to a nucleic acid encoding amiRNA. In certain embodiments, the miRNA comprises a 2- or 3-nucleotide5′ or 3′-overhang. In certain embodiments, the miRNA comprises a2-nucleotide 3′-overhang. In certain embodiments, the miRNA is anartificial miRNA.

The present invention provides a method of treating a subject with aneurodegenerative disease by administering to the subject a nucleicacid, an expression cassette, a vector, or a composition as describedherein so as to treat the neurodegenerative disease. In certainembodiments, the neurodegenerative disease is a trinucleotide repeatdisease. In certain embodiments, the neurodegenerative diseaseHuntington's Disease or spinocerebellar ataxia.

The present invention provides a method of suppressing the accumulationof a polyglutamine gene-encoded protein (such as huntingtin or ataxin-1)in a cell by introducing a nucleic acid molecules (e.g., a ribonucleicacid (RNA)) described herein into the cell in an amount sufficient tosuppress accumulation of huntingtin or ataxin-1 in the cell. In certainembodiments, the accumulation of huntingtin or ataxin-1 is suppressed byat least 10%. In certain embodiments, the accumulation of huntingtin orataxin-1 is suppressed by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90% 95%, or 99%. In certain embodiments, the suppression of theaccumulation of the protein is in an amount sufficient to cause atherapeutic effect, e.g., to reduce the formation of tangles.

The present invention provides a method of preventing cytotoxic effectsof mutant huntingtin or ataxin-1 in a cell by introducing a nucleic acidmolecules (e.g., a ribonucleic acid (RNA)) described herein into thecell in an amount sufficient to suppress accumulation of huntingtin orataxin-1. In certain embodiments, the nucleic acid molecules preventscytotoxic effects of huntingtin or ataxin-1, e.g., in a neuronal cell.

The present invention provides a method to inhibit expression of ahuntingtin or ataxin-1 gene in a cell by introducing a nucleic acidmolecule (e.g., a ribonucleic acid (RNA)) described herein into the cellin an amount sufficient to inhibit expression of the huntingtin orataxin-1, and wherein the RNA inhibits expression of the huntingtin orataxin-1 gene. In certain embodiments, the huntingtin or ataxin-1 isinhibited by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 95%,or 99%.

The present invention provides a method to inhibit expression of ahuntingtin or ataxin-1 gene in a mammal (e.g., a human or a non-humanmammal) by (a) providing a mammal containing a neuronal cell, whereinthe neuronal cell contains the huntingtin or ataxin-1 gene and theneuronal cell is susceptible to RNA interference, and the huntingtin orataxin-1 gene is expressed in the neuronal cell; and (b) contacting themammal with a ribonucleic acid (RNA) or a vector described herein,thereby inhibiting expression of the huntingtin or ataxin-1 gene. Incertain embodiments, the accumulation of huntingtin or ataxin-1 issuppressed by at least 10%. In certain embodiments, the huntingtin orataxin-1 is inhibited by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90% 95%, or 99%. In certain embodiments, the cell is located invivo in a mammal.

The present invention provides a viral vector comprising a promoter anda micro RNA (miRNA) shuttle containing an embedded siRNA specific for atarget sequence. In certain embodiments, the promoter is an induciblepromoter. In certain embodiments, the vector is an adenoviral,lentiviral, adeno-associated viral (AAV), poliovirus, HSV, or murineMaloney-based viral vector. In certain embodiments, the targetedsequence is a sequence associated with a condition amenable to siRNAtherapy, such as a neurodegenerative disease. An example ofneurodegenerative diseases is a trinucleotide-repeat disease, such as adisease associated with polyglutamine repeats. These diseases includeHuntington's disease and the spinocerebellar ataxias (SCA). Examples ofSCA diseases are SCA1, SCA2, SCA3, SCA6, SCA7, or SCA17. The targetsequence, in certain embodiments, is a sequence encoding ataxin-1 orhuntingtin.

The present invention provides a method of preventing cytotoxic effectsof neurodegenerative disease in a mammal in need thereof, by introducingthe vector encoding a miRNA described herein into a cell in an amountsufficient to suppress accumulation of a protein associated with theneurodegenerative disease, and wherein the RNA prevents cytotoxiceffects of neurodegenerative disease.

The present invention also provides a method to inhibit expression of aprotein associated with a neurodegenerative disease in a mammal in needthereof, by introducing the vector encoding a miRNA described hereininto a cell in an amount sufficient to inhibit expression of the proteinassociated with the neurodegenerative disease, wherein the RNA inhibitsexpression of the protein associated with the neurodegenerative disease.The protein associated with the neurodegenerative disease is inhibitedby at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 95%, or 99%.

This invention relates to compounds, compositions, and methods usefulfor modulating Huntington's Disease (also referred to as huntingtin,htt, or HD) gene expression using short interfering nucleic acid (siRNA)molecules. This invention also relates to compounds, compositions, andmethods useful for modulating the expression and activity of other genesinvolved in pathways of HD gene expression and/or activity by RNAinterference (RNAi) using small nucleic acid molecules. In particular,the instant invention features small nucleic acid molecules, such asshort interfering nucleic acid (siNA), short interfering RNA (siRNA),double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA(shRNA) molecules and methods used to modulate the expression HD genes.A siRNA molecule of the instant invention can be, e.g., chemicallysynthesized, expressed from a vector or enzymatically synthesized.

As used herein when a claim indicates an RNA “corresponding to” it ismeant the RNA that has the same sequence as the DNA, except that uracilis substituted for thymine.

In certain embodiments of the present invention, the alleles of thetargeted gene may differ by seven or fewer nucleotides (e.g., 7, 6, 5,4, 3, 2 or 1 nucleotides). For example the alleles may differ by onlyone nucleotide. Examples of targeted gene transcripts includetranscripts encoding a beta-glucuronidase, TorsinA, Ataxin-3, Tau, orhuntingtin. The targeted genes and gene products (i.e., a transcript orprotein) may be from different species of organisms, such as a mouseallele or a human allele of a target gene.

In one embodiment, the present invention further provides a method ofperforming gene silencing in a mammal or mammalian cell by administeringto the mammal an isolated miRNA or shRNA molecule, wherein the miRNA orshRNA silences only one, or both, alleles of the targeted gene (forexample the wild type and mutant alleles of HD gene) in the mammal ormammalian cell. In one example, the gene is a beta-glucuronidase gene.The alleles may be murine-specific and human-specific alleles ofbeta-glucuronidase. Examples of gene transcripts include an RNAtranscript complementary to TorsinA, Ataxin-3, huntingtin or Tau. Thetargeted gene may be a gene associated with a condition amenable tosiRNA therapy. For example, the condition amenable to siRNA therapycould be a disabling neurological disorder.

“Neurological disease” and “neurological disorder” refer to bothhereditary and sporadic conditions that are characterized by nervoussystem dysfunction, and which may be associated with atrophy of theaffected central or peripheral nervous system structures, or loss offunction without atrophy. A neurological disease or disorder thatresults in atrophy is commonly called a “neurodegenerative disease” or“neurodegenerative disorder.” Neurodegenerative diseases and disordersinclude, but are not limited to, amyotrophic lateral sclerosis (ALS),hereditary spastic hemiplegia, primary lateral sclerosis, spinalmuscular atrophy, Kennedy's disease, Alzheimer's disease, Parkinson'sdisease, multiple sclerosis, and repeat expansion neurodegenerativediseases, e.g., diseases associated with expansions of trinucleotiderepeats such as polyglutamine (polyQ) repeat diseases, e.g.,Huntington's disease (HD), spinocerebellar ataxia (SCA1, SCA2, SCA3,SCA6, SCA7, and SCA17), spinal and bulbar muscular atrophy (SBMA),dentatorubropallidoluysian atrophy (DRPLA). An example of a disablingneurological disorder that does not appear to result in atrophy is DYT1dystonia. The gene of interest may encode a ligand for a chemokineinvolved in the migration of a cancer cell, or a chemokine receptor.

The present invention further provides a method of substantiallysilencing a target gene of interest or targeted allele for the gene ofinterest in order to provide a therapeutic effect. As used herein theterm “substantially silencing” or “substantially silenced” refers todecreasing, reducing, or inhibiting the expression of the target gene ortarget allele by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% to 100%. As used herein theterm “therapeutic effect” refers to a change in the associatedabnormalities of the disease state, including pathological andbehavioral deficits; a change in the time to progression of the diseasestate; a reduction, lessening, or alteration of a symptom of thedisease; or an improvement in the quality of life of the personafflicted with the disease. Therapeutic effects can be measuredquantitatively by a physician or qualitatively by a patient afflictedwith the disease state targeted by the siRNA. In certain embodimentswherein both the mutant and wild type allele are substantially silenced,the term therapeutic effect defines a condition in which silencing ofthe wild type allele's expression does not have a deleterious or harmfuleffect on normal functions such that the patient would not have atherapeutic effect.

In one embodiment, the present invention further provides a method ofsubstantially silencing both alleles (e.g., both mutant and wild typealleles) of a target gene. In certain embodiments, the targeting of bothalleles of a gene target of interest can confer a therapeutic effect byallowing a certain level of continued expression of the wild-type allelewhile at the same time inhibiting expression of the mutant (e.g.,disease associated) allele at a level that provides a therapeuticeffect. For example, a therapeutic effect can be achieved by conferringon the cell the ability to express siRNA as an expression cassette,wherein the expression cassette contains a nucleic acid encoding a smallinterfering RNA molecule (siRNA) targeted against both alleles, andwherein the expression of the targeted alleles are silenced at a levelthat inhibits, reduces, or prevents the deleterious gain of functionconferred by the mutant allele, but that still allows for adequateexpression of the wild type allele at a level that maintains thefunction of the wild type allele. Examples of such wild type and mutantalleles include without limitation those associated with polyglutaminediseases such as Huntington's Disease.

In one embodiment, the present invention further provides a method ofsubstantially silencing a target allele while allowing expression of awild-type allele by conferring on the cell the ability to express siRNAas an expression cassette, wherein the expression cassette contains anucleic acid encoding a small interfering RNA molecule (siRNA) targetedagainst a target allele, wherein expression from the targeted allele issubstantially silenced but wherein expression of the wild-type allele isnot substantially silenced.

In one embodiment, the present invention provides a method of treating adominantly inherited disease in an allele-specific manner byadministering to a patient in need thereof an expression cassette,wherein the expression cassette contains a nucleic acid encoding a smallinterfering RNA molecule (siRNA) targeted against a target allele,wherein expression from the target allele is substantially silenced butwherein expression of the wild-type allele is not substantiallysilenced.

In one embodiment, the present invention provides a method of treating adominantly inherited disease by administering to a patient in needthereof an expression cassette, wherein the expression cassette containsa nucleic acid encoding a small interfering RNA molecule (siRNA)targeted against both the mutant allele and the wild type allele of thetarget gene, wherein expression from the mutant allele is substantiallysilenced at a level that still allows for expression from the wild typeallele to maintain its function in the patient.

In one embodiment, the present invention provides a method of performinggene silencing in a mammal by administering to the mammal a vectorcontaining an expression cassette, wherein the expression cassettecontains a nucleic acid encoding at least one strand of a smallinterfering RNA molecule (siRNA) targeted against a gene of interest,wherein the siRNA silences one or both alleles of the gene.

In one embodiment, the present invention provides a method of screeningof allele-specific siRNA duplexes, involving contacting a cellcontaining a predetermined mutant allele with an siRNA with a knownsequence, contacting a cell containing a wild-type allele with an siRNAwith a known sequence, and determining if the mutant allele issubstantially silenced while the wild-type allele retains substantiallynormal activity.

In one embodiment, the present invention provides a method of screeningof specific siRNA duplexes, involving contacting a cell containing botha predetermined mutant allele and a predetermined wild-type allele withan siRNA with a known sequence, and determining if the mutant allele issubstantially silenced at a level that allows the wild-type allele toretain substantially normal activity.

In one embodiment, the present invention also provides a method ofscreening of allele-specific siRNA duplexes involving contacting a cellcontaining a predetermined mutant allele and a wild-type allele with ansiRNA with a known sequence, and determining if the mutant allele issubstantially silenced while the wild-type allele retains substantiallynormal activity.

In one embodiment, the present invention also provides a method fordetermining the function of an allele by contacting a cell containing apredetermined allele with an siRNA with a known sequence, anddetermining if the function of the allele is substantially modified.

In one embodiment, the present invention further provides a method fordetermining the function of an allele by contacting a cell containing apredetermined mutant allele and a wild-type allele with an siRNA with aknown sequence, and determining if the function of the allele issubstantially modified while the wild-type allele retains substantiallynormal function.

In one embodiment, the invention features a method for treating orpreventing Huntington's Disease in a subject or organism comprisingcontacting the subject or organism with a siRNA of the invention underconditions suitable to modulate the expression of the HD gene in thesubject or organism whereby the treatment or prevention of Huntington'sDisease can be achieved. In one embodiment, the HD gene target comprisesa mutant HD allele (e.g., an allele comprising a trinucleotide (CAG)repeat expansion). In one embodiment, the HD gene target comprises bothHD allele (e.g., an allele comprising a trinucleotide (CAG) repeatexpansion and a wild type allele). The siRNA molecule of the inventioncan be expressed from vectors as described herein or otherwise known inthe art to target appropriate tissues or cells in the subject ororganism.

In one embodiment, the invention features a method for treating orpreventing Huntington's Disease in a subject or organism comprising,contacting the subject or organism with a siRNA molecule of theinvention via local administration to relevant tissues or cells, such asbrain cells and tissues (e.g., basal ganglia, striatum, or cortex), forexample, by administration of vectors or expression cassettes of theinvention that provide siRNA molecules of the invention to relevantcells (e.g., basal ganglia, striatum, or cortex). In one embodiment, thesiRNA, vector, or expression cassette is administered to the subject ororganism by stereotactic or convection enhanced delivery to the brain.For example, U.S. Pat. No. 5,720,720 provides methods and devices usefulfor stereotactic and convection enhanced delivery of reagents to thebrain. Such methods and devices can be readily used for the delivery ofsiRNAs, vectors, or expression cassettes of the invention to a subjector organism, and is U.S. Pat. No. 5,720,720 is incorporated by referenceherein in its entirety. US Patent Application Nos. 2002/0141980;2002/0114780; and 2002/0187127 all provide methods and devices usefulfor stereotactic and convection enhanced delivery of reagents that canbe readily adapted for delivery of siRNAs, vectors, or expressioncassettes of the invention to a subject or organism, and areincorporated by reference herein in their entirety. Particular devicesthat may be useful in delivering siRNAs, vectors, or expressioncassettes of the invention to a subject or organism are for exampledescribed in US Patent Application No. 2004/0162255, which isincorporated by reference herein in its entirety. The siRNA molecule ofthe invention can be expressed from vectors as described herein orotherwise known in the art to target appropriate tissues or cells in thesubject or organism.

Methods of delivery of viral vectors include, but are not limited to,intra-arterial, intra-muscular, intravenous, intranasal and oral routes.Generally, AAV virions may be introduced into cells of the CNS usingeither in vivo or in vitro transduction techniques. If transduced invitro, the desired recipient cell will be removed from the subject,transduced with AAV virions and reintroduced into the subject.Alternatively, syngeneic or xenogeneic cells can be used where thosecells will not generate an inappropriate immune response in the subject.

Suitable methods for the delivery and introduction of transduced cellsinto a subject have been described. For example, cells can be transducedin vitro by combining recombinant AAV virions with CNS cells e.g., inappropriate media, and screening for those cells harboring the DNA ofinterest can be screened using conventional techniques such as Southernblots and/or PCR, or by using selectable markers. Transduced cells canthen be formulated into pharmaceutical compositions, described morefully below, and the composition introduced into the subject by varioustechniques, such as by grafting, intramuscular, intravenous,subcutaneous and intraperitoneal injection.

In one embodiment, for in vivo delivery, AAV virions are formulated intopharmaceutical compositions and will generally be administeredparenterally, e.g., by intramuscular injection directly into skeletal orcardiac muscle or by injection into the CNS.

In one embodiment, viral vectors of the invention are delivered to theCNS via convection-enhanced delivery (CED) systems that can efficientlydeliver viral vectors, e.g., AAV, over large regions of a subject'sbrain (e.g., striatum and/or cortex). As described in detail andexemplified below, these methods are suitable for a variety of viralvectors, for instance AAV vectors carrying therapeutic genes (e.g.,siRNAs).

Any convection-enhanced delivery device may be appropriate for deliveryof viral vectors. In one embodiment, the device is an osmotic pump or aninfusion pump. Both osmotic and infusion pumps are commerciallyavailable from a variety of suppliers, for example Alzet Corporation,Hamilton Corporation, Aiza, Inc., Palo Alto, Calif.). Typically, a viralvector is delivered via CED devices as follows. A catheter, cannula orother injection device is inserted into CNS tissue in the chosensubject. In view of the teachings herein, one of skill in the art couldreadily determine which general area of the CNS is an appropriatetarget. For example, when delivering AAV vector encoding a therapeuticgene to treat HD, the striatum is a suitable area of the brain totarget. Stereotactic maps and positioning devices are available, forexample from ASI Instruments, Warren, Mich. Positioning may also beconducted by using anatomical maps obtained by CT and/or MRI imaging ofthe subject's brain to help guide the injection device to the chosentarget. Moreover, because the methods described herein can be practicedsuch that relatively large areas of the brain take up the viral vectors,fewer infusion cannula are needed. Since surgical complications arerelated to the number of penetrations, the methods described herein alsoserve to reduce the side effects seen with conventional deliverytechniques.

In one embodiment, pharmaceutical compositions will comprise sufficientgenetic material to produce a therapeutically effective amount of thesiRNA of interest, i.e., an amount sufficient to reduce or amelioratesymptoms of the disease state in question or an amount sufficient toconfer the desired benefit. The pharmaceutical compositions may alsocontain a pharmaceutically acceptable excipient. Such excipients includeany pharmaceutical agent that does not itself induce the production ofantibodies harmful to the individual receiving the composition, andwhich may be administered without undue toxicity. Pharmaceuticallyacceptable excipients include, but are not limited to, sorbitol,Tween80, and liquids such as water, saline, glycerol and ethanol.Pharmaceutically acceptable salts can be included therein, for example,mineral acid salts such as hydrochlorides, hydrobromides, phosphates,sulfates, and the like; and the salts of organic acids such as acetates,propionates, malonates, benzoates, and the like. Additionally, auxiliarysubstances, such as wetting or emulsifying agents, pH bufferingsubstances, and the like, may be present in such vehicles. A thoroughdiscussion of pharmaceutically acceptable excipients is available inREMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991).

As is apparent to those skilled in the art in view of the teachings ofthis specification, an effective amount of viral vector which must beadded can be empirically determined. Administration can be effected inone dose, continuously or intermittently throughout the course oftreatment. Methods of determining the most effective means and dosagesof administration are well known to those of skill in the art and willvary with the viral vector, the composition of the therapy, the targetcells, and the subject being treated. Single and multipleadministrations can be carried out with the dose level and pattern beingselected by the treating physician.

It should be understood that more than one transgene could be expressedby the delivered viral vector. Alternatively, separate vectors, eachexpressing one or more different transgenes, can also be delivered tothe CNS as described herein. Furthermore, it is also intended that theviral vectors delivered by the methods of the present invention becombined with other suitable compositions and therapies.

The present invention further provides an miRNA or shRNA, an expressioncassette and/or a vector as described herein for use in medicaltreatment or diagnosis.

The present invention provides the use of an miRNA or shRNA, anexpression cassette and/or a vector as described herein to prepare amedicament useful for treating a condition amenable to RNAi in ananimal, e.g., useful for treating Huntington's Disease.

The present invention also provides a nucleic acid, expression cassette,vector, or composition of the invention for use in therapy.

The present invention also provides a nucleic acid, expression cassette,vector, or composition of the invention for treating, e.g., for use inthe prophylactic or therapeutic treatment of, a neurodegenerativedisease.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts modified human mir-30 containing sequences specific forseveral genes of interest. Mir-30 (SEQ ID NO:1), miSCA1 (SEQ ID NO:2),shSCA1 (SEQ ID NO:3), miJNK (SEQ ID NO:4), and miHTT (SEQ ID NO:5).

FIG. 2. The target gene (in this case Ataxin-1, also called SCA1) wascloned, and the SCA1 miRNA was also generated.

FIG. 3. Artificial RNAi target constructs were generated in bothdirections.

FIGS. 4A-4C. Disparate strand-biasing confounds shRNA and artificialmiRNA comparisons. (FIG. 4A) Small transcript northern blot performed at48 h post-transfection of HD2.1 RNAi expression plasmids in HEK293 cellsshows improved yield of processed antisense RNA (AS) from CMV-drivenartificial miRNA variants 1 and 2 (miV1, miV2) relative to the U6-drivenfirst-generation shHD2.1. Pre-designates the precursor stem-loop. (FIG.4B) Q-PCR analysis for endogenous HD mRNA levels performed 48 h aftertransfection of HD2.1 RNAi expression plasmids into HEK293 cells.Results were normalized to GAPDH mRNA levels and are shown as mean±S.E.Mrelative to mock-treated samples (n=3, *=P<0.05). (FIG. 4C)Strand-biasing of U6-driven HD2.1 RNAi vectors. Strand-biasing wasassessed by measuring luciferase activity from reporters containingeither sense (intended; binds RNAi antisense) or antisense (unintended;binds RNAi sense) target sequences in the 3′UTR (FIG. 18C). RNAireporter and RNAi expression plasmids were co-transfected into HEK293cells, and Dual-Glo® Luciferase assays were performed at 24 h. Resultsare shown as mean±S.E.M (n=4) relative to mock-treated controls anddemonstrate that shHD2.1 preferentially loads the unintended siRNAstrand while miHD2.1 more often loads the intended strand.

FIG. 5. Design of 2^(nd) generation shRNA molecules.

FIGS. 6A-6C. A. shRNA variants were generated to assess the effects of5′ or 3′ modifications. B. Processing was observed by small transcriptnorthern blot 48 h post-transfection of shRNA-expression plasmids. C.Silencing of co-transfected artificial luciferase target 24 h followingtransfection.

FIGS. 7A-7B. A. Small transcript northern performed 48 hpost-transfection of eGFP RNAi in 293 cells. Probe: eGFP senseoligonucleotide. B. eGFP RNAi vs. siChk2-eGFP Target(6:1). Dual-Glo®luciferase assay was performed 24 h post-transfection of RNAi:Targetplasmids in 293 cells. Shown relative to mock RNAi.

FIG. 8. Comparison of 2^(nd) generation shRNA molecules and miRNAmolecules.

FIGS. 9A and 9B. Results of studies on the safety of RNAi vectors. FIG.9A shows a Spike Safety Study, and FIG. 9B shows a gene silencing study.

FIGS. 10A-10D. A. Differentiating C2C12 cells induces miR-1 and MHCexpression. B. Vector used to compare RNAi strategies. C. RNAi andsiCheck2 miR-1 luciferase reporter were co-transfected into C2C12 cellswhich were then differentiated for 72 hours and dual-luciferase assaywas performed. Results are shown relative to siCheck2 alone. D. RNAiplasmids were transfected and cells were differentiated for 72 hours.shRNA-treated cells showed decreased cell viability as observed byfluorescence and quantified by MTS assay.

FIG. 11. In vivo safety of RNAi vectors in muscle. miReporter andGFP:U6.RNAi (shRNA:Left or miRNA:Right) plasmids were co-electroporatedinto the tibialis anterior of the animals. IVIS Imaging for Firefly orRenilla Luciferase and GFP was examined.

FIGS. 12A-12B. A. siCheck2 miReporters (containing a perfect miRNAtarget site located in the 3′UTR of Firefly Luciferase) wereelectroporated into the tibialis anterior muscle. IVIS imaging wasperformed 48 later to measure the amount of Firefly luciferase activity.Results confirm the use of miReporters in vivo. miR-1 siCheck2 reporterwas used in subsequent experiments. B. pGFP:U6.RNAi and siCheck2 miR-1reporter expression plasmids were co-electroporated at varying doses(Lo=1 μg RNAi: 1 μg miReporter and Hi=10 μg RNAi: 1 μg miReporter) intothe tibialis anterior muscle. shRNAs were delivered to the left leg andmiRNAs to the right leg. IVIS imaging was performed at varioustime-points to measure Firefly luciferase activity.

FIGS. 13A-13B. Q-PCR was performed for mouse HD (FIG. 13A) and CD11b(FIG. 13B). Northern blots were also prepared for RNAi. The Q-PCRresults were normalized to GAPDH mRNA levels and are shown relative touninjected striatum. High-level expression from shRNA likely explainsthe observed toxicity.

FIG. 14. miRNA shuttle cloning strategy.

FIG. 15. Generation of miRNA molecules (exemplary miRNA at the left ofthe figure is SEQ ID NO:6).

FIG. 16. Vector sequences are depicted in this Figure. Transcriptionstart sites are bold and underlined. Restriction enzymes used in thecloning process are indicated. The underlined sequences within “Oligos”represent the annealing portion. Predicted miRNA and shRNA structuresare based on mFOLD analysis. Arrows indicate the major Drosha (left) andDicer (right) cleavage sites.

FIG. 17. Basic miRNA Structure of mi-Variant 2. 5′ flanking sequence(bold text), siRNA sequence (italics), Loop (normal text), and 3′flanking sequence (bold italics).

FIGS. 18A-18E. Optimization of the human miR-30 shuttle. (FIG. 18A)General structures of shRNAs and artificial miRNAs (Ns correspond to thesiRNA-duplex region with sense and antisense being 5′ and 3′respectively). Here, the antisense sequences are designed to targetSCA1, HD or GFP transcripts. Hash marks indicate the known major Droshaand Dicer cleavage sites of human miR-30. Processing sites of manyshRNAs are unknown and vary based on the presence of short flankingsequences. *, boxed sequence is for orientation purposes in the panel.(FIG. 18B) Artificial miRNA variants were generated by altering thenearby flanking sequences, and portions of the predicted mFOLDstructures within the stem-base are shown. Instability (i.e.single-stranded nature) within the grey-shaded region promotes Droshabinding and cleavage. These variants contain identical RNAi sequencesand structures in regions above the grey-shaded box. (FIG. 18C) Cartoondepicting RNAi reporters, generated by inserting target sequences intothe 3′UTR of Renilla luciferase. Reporter plasmids also contain aFirefly luciferase expression cassette for normalization. (FIG. 18D)Silencing activity of miR-30 variants. Artificial miSCA1 variants andRNAi reporter expression plasmids were co-transfected into HEK293 cells,and Dual-Glo® Luciferase assays were performed after 24 h. Results oftwo independent experiments (each n=3) are shown relative tomock-treated (i.e., promoter only) controls and demonstrate that variant2 (miV2) is the most effective artificial miRNA (even more effectivethan human miR-30, **=P<0.01). (FIG. 18E) Small transcript northern blotwas performed at 48 h post-transfection of miRNA variant expressionplasmids into HEK293 cells. Results show that miV2 yields more matureantisense RNA (SCA1 AS) compared to the other artificial miRNA variantsincluding the natural miR-30 shuttle.

FIG. 19 provides additional miRNA sequences that were used to targeteither HD or SCA1. These are the predicted RNA stem loop structures thatcontain the active RNAi sequences. The active antisense strand of theembedded siRNA sequence is underlined.

FIGS. 20A-20G provide an illustration of miRNA shuttles of the presentinvention. FIG. 20A depicts a primary miRNA transcript (pri-miRNA) withthe segments shown in 5′ to 3′ configuration. FIGS. 20B and 20C depictin further detail of alternative 5′-Flanking Regions with the segmentsshown in 5′ to 3′ configuration (light grey region with italics textshown in FIG. 20A is expanded in FIGS. 20B and 20C). FIGS. 20D and 20Edepict in further detail alternative 3′-Flanking Regions with thesegments shown in 5′ to 3′ configuration (dark grey region with boldtext shown in FIG. 20A is expanded in FIGS. 20D and 20E). FIG. 20Fprovides an exemplary artificial miRNA molecule.

FIGS. 21A-21C. shRNA processing and silencing efficiency isoverhang-dependent. (FIG. 21A) Diagrams depicting the various 5′ and 3′overhangs tested on identical shRNA stem-loops. (FIG. 21B) Plasmidsexpressing the shRNA variants were transfected into HEK293 cells, andsmall transcript northern blot [probing for antisense (AS) or sense (S)sequences] with densitometry analysis (values below blots) was performed48 h later to assess shRNA processing efficiency (n=3). Results showthat 5′ overhang variants yield less precursor (Pre-) and antisense (AS)RNAs compared to the optimized shRNAs with U₂₋₄ 3′ overhangs derivedfrom Pol-III transcription termination. Appropriate strand-loading wasobserved for each shRNA variant (i.e., AS:Pre->S:Pre-). (FIG. 21C)Silencing of intended (left bar graph) or unintended (right bar graph)target strands was assessed by co-transfection of shRNA-variant and RNAiluciferase reporter expression plasmids into HEK293 cells, and Dual Glo®Luciferase assays were performed at 24 h. Results are shown as mean±S.D.(n=3) relative to mock-treated controls and confirm that sub-optimaloverhangs decrease silencing efficiency. Notably, each shRNApreferentially silenced the intended target (transfected at 1:20RNAi:Target) relative to the unintended target (transfected at 3:1RNAi:Target).

FIGS. 22A-22B. Design of comparable shRNA and artificial miRNA hairpins.Diagram depicting the design of hairpins for a fair comparison scheme.Relevant cleavage sites mapped by 3′-RACE are shown (FIG. 27). Vectorswere designed to contain siRNAs targeting SCA1, GFP or HD transcripts(Ns). The stem and loop sequences are conserved. The “*” in FIG. 22Aindicates that the corresponding miRNA was modified to account for shRNArequirements. The mU6 promoter transcription starts at G (indicated byan arrow in FIG. 22B) and terminates leaving a 3′-U₂₋₄ overhang (FIG.22B shows 3′-U₂), which is optimal for recognition by downstream RNAimachinery. The Dicer cut sites are indicated with darker bars near theloop regions, and the Drosha cut site is indicated by lighter bars inFIG. 22A.

FIGS. 23A-23C. Comparable shRNA- and miRNA-based vectors exhibitappropriate strand-biasing. (FIGS. 23A-C) Strand-biasing of SCA1, GFP,and HD RNAi vectors respectively. Strand-biasing was assessed usingluciferase reporters containing either sense (intended) or antisense(unintended) target sequences. RNAi luciferase reporter and RNAiexpression plasmids were co-transfected into HEK293 cells, and Dual-Glo®Luciferase assays were performed at 24 h. Results of duplicateexperiments (each n=3) are shown as mean±S.E.M relative to mock-treatedcontrols and demonstrate that the artificial miRNA and shRNA vectorsexhibit appropriate strand-biasing.

FIGS. 24A-24E. shRNAs are more potent than artificial miRNAs in vitro.(FIG. 24A) RNAi and RNAi luciferase reporter plasmids wereco-transfected into HEK293 cells to assess gene silencing. Dual Glo®Luciferase assays were performed at 24 h and results, shown asmean±S.E.M relative to mock-treated controls, were compiled from severalexperiments (4 GFP, 4 SCA1 and 2 HD; each n=3). Dose is indicated asRNAi:Target. P<0.001 and P<0.05 for 1:1 and 3:1 doses respectively.(FIGS. 24B, 24C) Plasmids expressing RNAi targeting endogenous SCA1 orHD were transfected into HEK293 cells, and Q-PCR analysis was performedat 48 h to measure reduction of endogenous transcripts. SCA1 and HD mRNAlevels were normalized to GAPDH or 18S rRNA and are shown as mean±S.E.M(n≧3, *=P<0.05, ***=P<0.001) relative to mock-treated controls. (FIG.24D) GFP RNAi and eGFP expression plasmids were co-transfected intoHEK293 cells, and fluorescence levels were evaluated 48 h later. Resultsare shown as mean±S.E.M (n=4, **=P<0.01) relative to SCA1 RNAi-treatedcontrols. (FIG. 24E) shRNA and artificial miRNA expression plasmids weretransfected into HEK293 cells, and small transcript northern blot wasperformed at 48 h to assess RNAi expression and processing(Pre-=precursor, AS=antisense RNA). Results show that shRNAs yield morethan 4-fold mature antisense RNA, relative to artificial miRNAs,independent of RNAi target sequence. These results were consistent amongtriplicate blots for each RNAi vector-pair.

FIGS. 25A-25B. shRNAs are more potent than artificial miRNAs in vivo.Gene silencing efficacy in vivo was compared by co-electroporating SCA1RNAi and RNAi luciferase reporter plasmids into tibialis anteriormuscles of 6-8 week-old mice. Low and high doses are 1:1 and 10:1(RNAi:Target) ratios respectively. Renilla luciferase activity wasmeasured in vivo using bioluminescence imaging after 8 d. Representative“heat-map” images are shown (FIG. 25A) along with quantitative analysis(FIG. 25B) represented as mean±S.E.M (n=4; P<0.05 within each dose).Similar silencing trends were also observed at 4 d post-treatment (datanot shown).

FIGS. 26A-26B. (FIG. 26A) CMV- or U6-driven artificial miRNA vectorstargeting SCA1 were transfected into HEK293 cells, and small transcriptnorthern blot was performed at 48 h to assess RNAi expression andprocessing (AS=antisense siRNA). (FIG. 26B) RNAi and RNAi luciferasereporter plasmids were co-transfected into HEK293 cells to assess genesilencing. Dual Glo® Luciferase assays were performed at 24 h andresults, shown as mean±S.E.M relative to mock-treated controls, werecompiled from several experiments (3 SCA1, 3 GFP; each n=3). Dose isindicated as RNAi:Target and P<0.01 within each dose.

FIG. 27. Mapping cleavage sites for corresponding shRNA and artificialmiRNA vectors. HEK293 cells were transfected with shSCA1 or miSCA1expression plasmids and 3′-RACE was performed on RNA harvested 48 hlater to identify the 3′ ends of antisense (AS) or sense (S) SCA1 smallRNAs derived from these vectors. For each vector, the 10-12 analyzedsequences per strand are shown. Notably, each represented sequence ispresent in both shSCA1- or miSCA1-treated samples, and the mostprevalent species (shaded grey box) was shared. Lowercase nucleotidesindicate bases that were ambiguous due to the use of an anchoredoligo-dT primer during first-strand cDNA synthesis. FIG. 27 includes SEQID NOs:84-135.

FIG. 28. Artificial miRNA cloning strategy. Overlapping DNAoligonucleotides are designed to generate a basic miR-30 stem-loopcontaining siRNA sense and antisense sequences along with the necessaryelements within the stem-base known to direct efficient Drosha cleavage.Oligonucleotides are annealed and extended with DNA polymerase togenerate the dsDNA encoding the artificial miRNA flanked by restrictionenzyme sites. This cassette is digested and cloned to expression vectorswhich provide additional flanking sequences that can influence theprocessing efficiency. “Term.” refers to the transcription terminator(e.g., polyA signal or 6T's for CMV and U6 promoters (shown as arrow)respectively).

FIG. 29. Comparison of an exemplary shRNA (SEQ ID NO: 136) and miRNA(SEQ ID NO:137) that produce an equivalent siRNA molecule (SEQ IDNOs:138-139).

FIGS. 30A-30E. FIG. 30A shows that shSCA1 significantly decreased thefunction of miGFP. FIG. 30B shows that miSCA1 demonstrated similarsilencing efficacy as a low dose of shSCA1 when targeting the SCA1 RNAiluciferase report. FIGS. 30C, 30D show reciprocal experiments where theeffect of GFP RNAi competitors (shGFP or miGFP) on miSCA1 activity wasevaluated in parallel with GFP RNAi efficacy. FIG. 30E shows that miGFPbiogenesis was severely disrupted in the presence of shSCA1 expressionvectors at low and high doses.

FIGS. 31A-31E. FIGS. 31A, 31B show the measurement of the activity of aluciferase reporter for miR-1 function in undifferentiated anddifferentiated C2C12 cells. FIG. 31C shows measurements of theelongation of differentiated C2C12 cells following transfection withshRNA or artificial miRNA expression plasmids that co-express CMV-driverhrGFP. FIG. 31D shows the relative lengths of MHC+GFP+ cells. FIG. 31Eshows that the elongation process was significantly reduced in C2C12cells transfected with shSCA1-expressing plasmids, nut not thoseexpressing miSCA1.

FIG. 32. The survival of RNAi-transfected C2C12 cells was assessed bymonitoring the co-expression of hrGFP by fluorescence microscopy overtime.

FIG. 33. This figure shows the generation of AAV serotype 2/1-expressingU6 driven shSCA1 or miSCA1.

FIG. 34. shRNAs targeting sequences across the huntingtin gene. shRNAsequences are named for the targeted exon. For example, sh1.10 targetsexon 1, and it was the 10^(th) shRNA designed. Intervening numbers(e.g., sh1.5) targeted sequences between 1.4 and 1.8, but were specificto human sequences only. Functionality was determined by QPCR andprotein dot blot performed 48 h post-transfection into HEK 293 cells.Three lead sequences (bold italics) were chosen for in vivo analysis inCAG140 knock in mice based on consistent and differential gene silencingin cell culture screens. sh2.1 was identified during a prior screen andshown to be efficacious in a mouse model of HD. It targets only humanhuntingtin.

FIGS. 35A-35C. In vitro screening of shRNAs targeting human HD and mouseHDh transcripts. (FIG. 35A) Thirty-five shRNAs (bars above cartoon)targeting conserved sequences (FIG. 34) spanning human Huntington'sdisease (HD) and mouse Huntington's Disease homolog (HDh) mRNAs weregenerated with consideration for sequences that promote proper loadingof the antisense strands into the RISC. Plasmids expressing U6-drivenshRNAs were transfected into HEK293 cells and HD gene silencing wasevaluated by QPCR and protein dot blot analyses 48 h post-transfection.(FIG. 35B) Three candidate shRNAs targeting sequences in exons 2 (sh2.4,SEQ ID NO:175), 8 (sh8.2, SEQ ID NO:176) and 30 (sh30.1, SEQ ID NO:177)were chosen for further study. (FIG. 35C) shRNA expression plasmids weretransfected into mouse C2C12 cells, and endogenous huntingtin proteinlevels were evaluated by western blot analyses 48 h post-transfection.Mismatch (mis) controls contain 4 base pair changes that render theshRNAs ineffective. Beta-catenin serves as the loading control.

FIGS. 36A-36D. HD shRNAs cause sequence-specific striatal toxicity inmice. FIG. 36A is a diagram of the recombinant AAV2/1 viral vectorscontaining shRNA and hrGFP expression cassettes. FIG. 36B showsphotomicrographs represent the rostral-to-caudal distribution ofhrGFP-positive cells in mouse brain following direct injection of virusinto the striatum. Scale bar=500 μm. (36C) QPCR analysis measuring HDhmRNA levels in shRNA-treated mouse striata demonstrates similarsilencing efficacies among sh2.4, sh8.2 and sh30.1. Mice were injectedinto the striatum with AAVsh2.4-GFP, AAVsh8.2-GFP, AAVsh30.1-GFP orAAV-GFP and RNA was harvested 4 months later. Immunohistochemistryrevealed that sh2.4 and sh30.1 induce striatal toxicity in mice (FIG.36D). Mice were injected with the indicated AAVshRNA-GFP or AAV-GFP intothe striatum, and histological analyses were performed on brainsharvested at 4 months post-treatment. Representative photomicrographsfor immunohistochemical staining of DARPP-32-positive neurons (toppanel, scale bar=500 um) and IbaI-positive microglia (bottom panel,scale bar=100 um) are shown for each treatment group.

FIG. 37. GFP-positive cells co-localize with neurons in the striatum.Immunofluorescent staining of GFP-positive cells (autofluorescence)throughout the striatum co-labeled with either RIP (top panel,oligodendrocyte marker), GFAP (middle panel, astrocyte marker) or NeuN(bottom panel, neuronal marker). Scale bar=20 um for eachphotomicrograph.

FIGS. 38A-38B. The non-toxic sh8.2 generates lower levels of processedantisense RNA. (FIG. 38A) Small transcript northern blot was performedto assess antisense RNA levels present in mouse striata treated with theindicated AAVshRNA-GFP. Left lanes: 2 separately treated striatal tissuesamples. Center and right lanes: positive controls loaded as standards[10-fold dilutions for both sense (center) or antisense (right)strands]. (FIG. 38B) Densitometry analysis was used to quantify therelative levels of HD antisense (AS) RNAs. Signals were quantified usingImage J Software and expression is shown as femtomoles/microgram totalRNA.

FIGS. 39A-39D. Artificial miRNAs mitigate striatal toxicity in mice.QPCR analyses were performed to measure mouse HDh (FIG. 39A) and CD11b(FIG. 39B) mRNA levels in AAV-RNAi-injected striata harvested 4 monthspost-treatment (NS=not significant). Results, shown relative touninjected striata, demonstrate that mi2.4 silences HD transcripts aseffectively as sh2.4, but avoids induction of CD11b, a marker formicroglial activation. (FIG. 39C) Small transcript northern blotanalysis for mature HD2.4 antisense (AS) RNAs present inAAV-RNAi-treated striatal lysates reveals a robust disparity between thelevels generated from sh2.4 and mi2.4 vectors. Ethidium bromide (EtBr)staining is shown as the loading control. (FIG. 39D) Histologicalanalyses demonstrate the improved safety profile of mi2.4. Mice wereinjected with the indicated AAV-RNAi-GFP viruses into the striatum andhistological analyses were performed on brains harvested at 4 monthspost-treatment. Photomicrographs representing hrGFP (top panel) andimmunohistochemical staining of DARPP-32-positive neurons (middle panel)and IbaI-positive microglia (bottom panel) are shown for each treatmentgroup. Scale bar=500 μm.

FIGS. 40A-40C. Artificial miRNAs naturally reduce precursor and matureinhibitory RNAs. (40A) Sequences and comparison of sh2.4 and mi2.4containing the core HD2.4 sequence (shaded boxes). Each transcriptstarts with the +1-G nucleotide natural to the U6 promoter. The majorDrosha and Dicer cleavage sites are shown by hash marks. (40B) HEK 293cells were transfected with HD2.4 RNAi expression plasmids at theindicated amounts, and small transcript northern blot was performed 48 hlater. Results demonstrate that sh2.4 generates abundant levels ofunprocessed precursor (Pre-) and processed antisense RNAs (2.4AS), evenat a 10-fold lower dose, relative to mi2.4. Ethidium bromide (EtBr)staining is shown as the loading control. (40C) HD 2.4 RNAi expressionplasmids were transfected into HEK 293 cells, and QPCR analysis wasperformed 48 h later to measure endogenous HD mRNA levels. Resultsdemonstrate that mi2.4 silences HD transcripts efficiently, relative tosh2.4, despite being expressed at considerably lower levels.

FIG. 41. Increased microglial activation in AAVsh2.4-GFP treated mice.Immunohistochemistry for the microglia marker, IbaI, performed onstriatal tissue sections from mice injected with either AAVsh2.4-GFP(bottom panel), AAVmi2.4-GFP (middle panel) or AAVmi2.4mis-GFP (toppanel). Both the AAV-injected (right panel) and uninjected (left panel)hemispheres are shown. Scale bar=100 um for each photomicrograph.

FIGS. 42A-42B. Targeting mutant huntingtin. FIG. 42A provides aschematic representation of the huntingtin (htt) gene. The intronsequences are the lightest bands, and the exon sequences are the secondlightest bands. The expanded CAG sequence (dark band) is localized inthe first exon of the Htt gene. FIG. 42B provides siRNA walking 5′ and3′. Sequences of short interfering RNA (siRNA) targeting 5′ and 3′ ofthe CAG-repeat region were generated to preferentially target the mutanthuntingtin allele.

FIGS. 43A-43B. Constructs to assess allele-specific silencing. Twoplasmids were generated expressing full-length wild type (FIG. 43A,pCMV-FLHtt 18Q-Flag) or mutant huntingtin (FIG. 43B, pCMV-FLHtt 83Q-V5).

FIGS. 44A-44C. shows Western blots and Q-PCR results for candidate siRNAsequences. FIG. 44A shows wild type Htt and FIG. 44B shows mutant Htt.As seen in FIG. 44C, siRNA sequence number 7 (S7) reduced mutant htt by40% and the wild type huntingtin by 6%.

FIG. 45 shows the results of miRNA shuttles for allele-specificsilencing of htt. Data represents the densitometry analysis of wild typeand mutant Htt expression for different protein lysates.

FIGS. 46A-46B. Dose response of mi7A1 sequence. FIG. 46A shows normalHtt, and FIG. 46B shows mutant Htt.

FIG. 47. Strand biasing of miR shuttles. Data represents relativeluciferase expression of the reporter constructs for each specificstrand after mi7 shuttle transfection. All data is compared to cellstransfected with each reporter constructs and a miRNA control (miGFP).

DETAILED DESCRIPTION OF THE INVENTION

RNA interference (RNAi) provides a promising approach for the treatmentof several human diseases. However, the safety of expressed vector basedRNAi-based therapies remains a concern. Safety concerns for vectorexpressed RNAi therapies arise as a result of off target toxicity.

The use of RNAi as a therapeutic is dependant upon the elucidation ofseveral factors including i) the delivery and persistence of the RNAiconstruct for effective silencing of the target gene sequence; ii) thedesign of the siRNA in order to achieve effective knock down or genesuppression of the target sequence, and iii) the optimal siRNAexpression system (shRNA or miRNA) for delivery of the therapeuticsiRNA. While many studies have evaluated the use of RNAi delivered aschemically synthesized oligonucleotide structures, for many clinicalconditions and disease states such as Huntington's Disease, it isbelieved that to achieve therapeutic benefit there is a need for longterm and or persistent high level expression of the therapeutic siRNA asachieved by endogenous production of expressed siRNA. To date, shRNA-and artificial miRNA-based strategies have been compared withconflicting results (Boden et al., 2004, Nucleic Acids Res 32:1154-1158; Silva et al., 2005, Nat Genet. 37: 1281-1288; Li et al.,2007, RNA 13: 1765-1774). The therapeutic utility of expressed RNAi isunresolved due to safety concerns as a result of off target toxicityarising from cellular responses to dsRNA (IFN-b, PKR, OAS1), saturationof RNAi machinery or silencing of off targets via partialcomplementarity with unintended mRNAs. Thus, there is an on-going needfor optimizing expressed RNAi vectors that are safe and effective.

shRNAs are comprised of stem-loop structures which are designed tocontain a 5′ flanking region, siRNA region segments, a loop region, a 3′siRNA region and a 3′ flanking region. Most RNAi expression strategieshave utilized short-hairpin RNAs (shRNAs) driven by strong polIII-basedpromoters. Many shRNAs have demonstrated effective knock down of thetarget sequences in vitro as well as in vivo, however, some shRNAs whichdemonstrated effective knock down of the target gene were also found tohave toxicity in vivo. A recently discovered alternative approach is theuse of artificial miRNAs (pri-miRNA scaffolds shuttling siRNA sequences)as RNAi vectors. Artificial miRNAs more naturally resemble endogenousRNAi substrates and are more amenable to Pol-II transcription (e.g.,allowing tissue-specific expression of RNAi) and polycistronicstrategies (e.g., allowing delivery of multiple siRNA sequences). Todate the efficacy of miRNA based vector systems compared to shRNA hasbeen confounded by conflicting results. Importantly, the question ofoff-target toxicity produced by the two systems has not been evaluated.

An important consideration for development of expressed siRNA is theconcept of “dosing” the host cell with the expressed siRNA construct.“Dosing” for an expressed siRNA in the context of the present inventionrefers to and can be dependant on the delivery vehicle (e.g., viral ornonviral), the relative amounts or concentration of the deliveryvehicle, and the strength and specificity of the promoter utilized todrive the expression of the siRNA sequence. In the present applicationthe inventors have directly compared the efficacy and off-targettoxicity of the expressed RNAi vectors under conditions where the shRNAsand miRNAs were delivered at equivalent dose by an AAV vector.

The inventors have developed artificial miRNA shuttle vectors thatincorporate the stem loop sequences contained in shRNAs withinmodifications of a naturally occurring human microRNA 30 sequence ormi30 sequence that serve to shuttle these small interfering RNA (siRNA)sequences. Unlike previously published reports, these miRNA shuttleswere subsequently compared to optimized shRNA constructs. The shRNAconstructs were optimized to contain sequences with the weakest basepairing near the 5′ end of the antisense or guide when compared to thesense or non-guide strand in order to allow for efficient processing andloading of the antisense into the RNAi-induced silencing complex (RISC).These optimized siRNAs were then compared to the artificial miRNAshuttle vectors containing the identical target sequences. The inventorsfound that optimized shRNAs, independent of siRNA sequence and targetsequence, generate more processed siRNAs and are more efficient atmediating gene silencing. However, northern blot analysis showed anoverabundance of unprocessed shRNAs as well as mature antisense RNAmolecules, whereas processing of the miRNA shuttles was highlyefficient. The inventors hypothesized that the unprocessed shRNAs mayarise due to saturation of the RNAi machinery and may result inadditional safety concerns due to off-target toxicity. In addition,while certain shRNAs were demonstrated to be potent gene silencers as aresult of overabundant or overexpression of shRNAs, they were alsooverly toxic when delivered in vivo to brains. An approach to reducetoxicity evaluated by the inventors was to lower the dose of the shRNAdelivered by lowering the viral titer injected, thereby decreasing thecopy number of the siRNA in the transduced cell, resulting in lowerexpression of the siRNA. However, lowering the dose in terms of viraltiter did not reduce off-target toxicity in the brain until the dose waslowered to levels that were not effective in target gene silencing.

The inventors evaluated whether generation of artificial miRNAs wouldreduce off target toxicity, thereby improving the relative safety ofsiRNA as a potential therapeutic. The inventors evaluated off targettoxicity of shRNA and miRNA vectors on the processing and function ofartificial miRNAs designed to mimic endogenous stem loops. Northern blotanalysis showed that shRNAs markedly inhibited processing of artificialmiRNAs, while miRNA shuttles had relatively no effect even at muchhigher doses. Similarly, shRNAs at low doses drastically reducedsilencing mediated by artificial miRNAs, whereas miRNA shuttles at highdoses only caused slight inhibition. Notably, silencing efficacies ofmiRNA shuttles (high dose) and shRNAs (low dose) were indistinguishable.These results suggest that shRNA-based vectors saturate cellular RNAimachinery substantially more than miRNA shuttles. Surprisingly,sequences that were found to have off-target toxicity in vivo in thecontext of a shRNA vector, when placed into the artificial miRNA vectorof the present invention, demonstrated attenuated off-target toxicityyet retained effective target gene silencing. Hence, the miRNA shuttlevector of the present invention provides a safer approach to delivertherapeutic RNAi in vivo.

MicroRNA Shuttles for RNAi

miRNAs are small cellular RNAs (˜22 nt) that are processed fromprecursor stem loop transcripts. Known miRNA stem loops can be modifiedto contain RNAi sequences specific for genes of interest. miRNAmolecules can be preferable over shRNA molecules because miRNAs areendogenously expressed. Therefore, miRNA molecules are unlikely toinduce dsRNA-responsive interferon pathways, they are processed moreefficiently than shRNAs, and they have been shown to silence 80% moreeffectively.

Also, the promoter roles are different for miRNA molecules as comparedto shRNA molecules. Tissue-specific, inducible expression of shRNAsinvolves truncation of polII promoters to the transcription start site.In contrast, miRNAs can be expressed from any polII promoter because thetranscription start and stop sites can be relatively arbitrary.

Treatment of Diseases

The dominant polyglutamine expansion diseases, which includeSpinocerebellar ataxia type 1 (SCA1) and Huntington's disease (HD), areprogressive, untreatable neurodegenerative disorders. In inducible mousemodels of SCA1 and HD, repression of mutant allele expression improvesdisease phenotypes. Thus, therapies designed to inhibit disease geneexpression would be beneficial. In studies presented herein, the abilityof RNA interference (RNAi) to inhibit polyglutamine-inducedneurodegeneration caused by mutant ataxin-1 was evaluated in a mousemodel of SCA1. Upon intracerebellar injection, recombinant AAV vectorsexpressing shRNAs profoundly improved motor coordination, restoredcerebellar morphology, and resolved characteristic ataxin-1 inclusionsin Purkinje cells of SCA1 mice. The present invention thus providesmethods of using RNAi in vivo to treat dominant neurodegenerativediseases. “Treating” as used herein refers to ameliorating at least onesymptom of, curing and/or preventing the development of a disease or acondition.

In certain embodiment of the invention, siRNAs are employed to inhibitexpression of a target gene. By “inhibit expression” is meant to reduce,diminish or suppress expression of a target gene. Expression of a targetgene may be inhibited via “gene silencing.” Gene silencing refers to thesuppression of gene expression, e.g., transgene, heterologous geneand/or endogenous gene expression, which may be mediated throughprocesses that affect transcription and/or through processes that affectpost-transcriptional mechanisms. In some embodiments, gene silencingoccurs when siRNA initiates the degradation of the mRNA transcribed froma gene of interest in a sequence-specific manner via RNA interference,thereby preventing translation of the gene's product.

The reference to siRNAs herein is meant to include shRNAs and othersmall RNAs that can or are capable of modulating the expression of atargeted gene, e.g., the HD gene, for example via RNA interference. Suchsmall RNAs include without limitation, shRNAs and microRNAs (miRNAs).

Disclosed herein is a strategy that results in substantial silencing oftargeted alleles via siRNA. Use of this strategy results in markedlydiminished in vitro and in vivo expression of targeted alleles. Thisstrategy is useful in reducing expression of targeted alleles in orderto model biological processes or to provide therapy for human diseases.For example, this strategy can be applied to a major class ofneurodegenerative disorders, the polyglutamine diseases, as isdemonstrated by the reduction of polyglutamine aggregation in cellsfollowing application of the strategy. As used herein the term“substantial silencing” means that the mRNA of the targeted allele isinhibited and/or degraded by the presence of the introduced siRNA, suchthat expression of the targeted allele is reduced by about 10% to 100%as compared to the level of expression seen when the siRNA is notpresent. Generally, when an allele is substantially silenced, it willhave at least 40%, 50%, 60%, to 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%,77%, 78%, to 79%, generally at least 80%, e.g., 81%-84%, at least 85%,e.g., 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or even 100% reduction expression as compared to when the siRNA isnot present. As used herein the term “substantially normal activity”means the level of expression of an allele when an siRNA has not beenintroduced to a cell.

Dominantly inherited diseases, including polyQ neurodegenerativedisorders, are ideal candidates for siRNA-based therapy. The polyQneurodegenerative disorders include at least nine inherited disorderscaused by CAG repeat expansions that encode polyQ in the diseaseprotein. PolyQ expansion confers a dominant toxic property on the mutantprotein that is associated with aberrant accumulation of the diseaseprotein in neurons. PolyQ diseases are progressive, ultimately fataldisorders that typically begin in adulthood. Huntington disease (HD) isthe best known polyQ disease, but at least seven hereditary ataxias andone motor neuron disease are also due to CAG repeat/polyQ expansion.Although the clinical features and patterns of neuronal degenerationdiffer among the diseases, increasing evidence suggests that polyQdiseases share important pathogenic features. In particular, expansionof the CAG repeat/polyQ domain confers upon the encoded protein adominant toxic property. Thus, as a therapeutic strategy, efforts tolower expression of the mutant gene product prior to cell death could behighly beneficial to patients.

The polyQ neurodegenerative disorders include at least nine diseasescaused by CAG repeat expansions that encode polyQ in the diseaseprotein. PolyQ expansion confers a dominant toxic property on the mutantprotein that is associated with aberrant accumulation of the diseaseprotein in neurons. In FTDP-17, Tau mutations lead to the formation ofneurofibrillary tangles accompanied by neuronal dysfunction anddegeneration. The precise mechanisms by which these mutant proteinscause neuronal injury are unknown, but considerable evidence suggeststhat the abnormal proteins themselves initiate the pathogenic process.Accordingly, eliminating expression of the mutant protein by siRNA orother means slows or prevents disease. However, because many dominantdisease genes also encode essential proteins siRNA-mediated approacheswere developed that selectively inactivate mutant alleles, whileallowing continued expression of the wild type proteins ataxin-3 andhuntingtin.

I. RNA Interference (RNAi) Molecules

An “RNA interference,” “RNAi,” “small interfering RNA” or “shortinterfering RNA” or “siRNA” or “short hairpin RNA” or “shRNA” molecule,or “miRNA” is a RNA duplex of nucleotides that is targeted to a nucleicacid sequence of interest, for example, ataxin-1 or huntingtin (htt). Asused herein, the term “siRNA” is a generic term that encompasses thesubset of shRNAs and miRNAs. An “RNA duplex” refers to the structureformed by the complementary pairing between two regions of a RNAmolecule. siRNA is “targeted” to a gene in that the nucleotide sequenceof the duplex portion of the siRNA is complementary to a nucleotidesequence of the targeted gene. In certain embodiments, the siRNAs aretargeted to the sequence encoding ataxin-1 or huntingtin. In someembodiments, the length of the duplex of siRNAs is less than 30 basepairs. In some embodiments, the duplex can be 29, 28, 27, 26, 25, 24,23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11 or 10 base pairs inlength. In some embodiments, the length of the duplex is 19 to 25 basepairs in length. In certain embodiment, the length of the duplex is 19or 21 base pairs in length. The RNA duplex portion of the siRNA can bepart of a hairpin structure. In addition to the duplex portion, thehairpin structure may contain a loop portion positioned between the twosequences that form the duplex. The loop can vary in length. In someembodiments the loop is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24 or 25 nucleotides in length. In certainembodiments, the loop is 18 nucleotides in length. The hairpin structurecan also contain 3′ and/or 5′ overhang portions. In some embodiments,the overhang is a 3′ and/or a 5′ overhang 0, 1, 2, 3, 4 or 5 nucleotidesin length.

The transcriptional unit of a “shRNA” is comprised of sense andantisense sequences connected by a loop of unpaired nucleotides. shRNAsare exported from the nucleus by Exportin-5, and once in the cytoplasm,are processed by Dicer to generate functional siRNAs. “miRNAs”stem-loops are comprised of sense and antisense sequences connected by aloop of unpaired nucleotides typically expressed as part of largerprimary transcripts (pri-miRNAs), which are excised by the Drosha-DGCR8complex generating intermediates known as pre-miRNAs, which aresubsequently exported from the nucleus by Exportin-5, and once in thecytoplasm, are processed by Dicer to generate functional siRNAs.“Artificial miRNA” or an “artificial miRNA shuttle vector”, as usedherein interchangably, refers to a primary miRNA transcript that has hada region of the duplex stem loop (at least about 9-20 nucleotides) whichis excised via Drosha and Dicer processing replaced with the siRNAsequences for the target gene while retaining the structural elementswithin the stem loop necessary for effective Drosha processing. The term“artificial” arises from the fact the flanking sequences (˜35nucleotides upstream and ˜40 nucleotides downstream) arise fromrestriction enzyme sites within the multiple cloning site of the siRNA.As used herein the term “miRNA” encompasses both the naturally occurringmiRNA sequences as well as artificially generated miRNA shuttle vectors.

The siRNA can be encoded by a nucleic acid sequence, and the nucleicacid sequence can also include a promoter. The nucleic acid sequence canalso include a polyadenylation signal. In some embodiments, thepolyadenylation signal is a synthetic minimal polyadenylation signal ora sequence of six Ts.

“Off-target toxicity” refers to deleterious, undesirable, or unintendedphenotypic changes of a host cell that expresses or contains an siRNA.Off-target toxicity may result in loss of desirable function, gain ofnon-desirable function, or even death at the cellular or organismallevel. Off-target toxicity may occur immediately upon expression of thesiRNA or may occur gradually over time. Off-target toxicity may occur asa direct result of the expression siRNA or may occur as a result ofinduction of host immune response to the cell expressing the siRNA.Without wishing to be bound by theory, off-target toxicity is postulatedto arise from high levels or overabundance of RNAi substrates within thecell. These overabundant or overexpressed RNAi substrates, includingwithout limitation pre- or pri RNAi substrates as well as overabundantmature antisense-RNAs, may compete for endogenous RNAi machinery, thusdisrupting natural miRNA biogenesis and function. Off-target toxicitymay also arise from an increased likelihood of silencing of unintendedmRNAs (i.e., off-target) due to partial complementarity of the sequence.Off target toxicity may also occur from improper strand biasing of anon-guide region such that there is preferential loading of thenon-guide region over the targeted or guide region of the RNAi.Off-target toxicity may also arise from stimulation of cellularresponses to dsRNAs which include dsRNA (IFN-b, PKR, OAS1). “Decreasedoff target toxicity” refers to a decrease, reduction, abrogation orattenuation in off target toxicity such that the therapeutic effect ismore beneficial to the host than the toxicity is limiting or detrimentalas measured by an improved duration or quality of life or an improvedsign or symptom of a disease or condition being targeted by the siRNA.“Limited off target toxicity” or “low off target toxicity” is used torefer to an unintended undesirable phenotypic changes to a cell ororganism, whether detectable or not, that does not preclude or outweighor limit the therapeutic benefit to the host treated with the siRNA andmay be considered a “side effect” of the therapy. Decreased or limitedoff target toxicity may be determined or inferred by comparing the invitro analysis such as Northern blot or QPCR for the levels of siRNAsubstrates or the in vivo effects comparing an equivalent shRNA vectorto the miRNA shuttle vector of the present invention.

“Knock-down,” “knock-down technology” refers to a technique of genesilencing in which the expression of a target gene is reduced ascompared to the gene expression prior to the introduction of the siRNA,which can lead to the inhibition of production of the target geneproduct. The term “reduced” is used herein to indicate that the targetgene expression is lowered by 1-100%. In other words, the amount of RNAavailable for translation into a polypeptide or protein is minimized.For example, the amount of protein may be reduced by 10, 20, 30, 40, 50,60, 70, 80, 90, 95, or 99%. In some embodiments, the expression isreduced by about 90% (i.e., only about 10% of the amount of protein isobserved a cell as compared to a cell where siRNA molecules have notbeen administered). Knock-down of gene expression can be directed by theuse of dsRNAs or siRNAs.

“RNA interference (RNAi)” is the process of sequence-specific,post-transcriptional gene silencing initiated by siRNA. During RNAi,siRNA induces degradation of target mRNA with consequentsequence-specific inhibition of gene expression.

According to a method of the present invention, the expression ofhuntingtin or atxain-1 can be modified via RNAi. For example, theaccumulation of huntingtin or atxain-1 can be suppressed in a cell. Theterm “suppressing” refers to the diminution, reduction or elimination inthe number or amount of transcripts present in a particular cell. Forexample, the accumulation of mRNA encoding huntingtin or atxain-1 can besuppressed in a cell by RNA interference (RNAi), e.g., the gene issilenced by sequence-specific double-stranded RNA (dsRNA), which is alsocalled short interfering RNA (siRNA). These siRNAs can be two separateRNA molecules that have hybridized together, or they may be a singlehairpin wherein two portions of a RNA molecule have hybridized togetherto form a duplex.

A mutant protein refers to the protein encoded by a gene having amutation, e.g., a missense or nonsense mutation in one or both allelesof huntingtin or atxain-1. A mutant huntingtin or atxain-1 may bedisease-causing, i.e., may lead to a disease associated with thepresence of huntingtin or atxain-1 in an animal having either one or twomutant allele(s).

The term “gene” is used broadly to refer to any segment of nucleic acidassociated with a biological function. Thus, genes include codingsequences and/or the regulatory sequences required for their expression.For example, “gene” refers to a nucleic acid fragment that expressesmRNA, functional RNA, or specific protein, including regulatorysequences. “Genes” also include nonexpressed DNA segments that, forexample, form recognition sequences for other proteins. “Genes” can beobtained from a variety of sources, including cloning from a source ofinterest or synthesizing from known or predicted sequence information,and may include sequences designed to have desired parameters. An“allele” is one of several alternative forms of a gene occupying a givenlocus on a chromosome.

The term “nucleic acid” refers to deoxyribonucleic acid (DNA) orribonucleic acid (RNA) and polymers thereof in either single- ordouble-stranded form, composed of monomers (nucleotides) containing asugar, phosphate and a base that is either a purine or pyrimidine.Unless specifically limited, the term encompasses nucleic acidscontaining known analogs of natural nucleotides that have similarbinding properties as the reference nucleic acid and are metabolized ina manner similar to naturally occurring nucleotides. Unless otherwiseindicated, a particular nucleic acid sequence also encompassesconservatively modified variants thereof (e.g., degenerate codonsubstitutions) and complementary sequences, as well as the sequenceexplicitly indicated. Specifically, degenerate codon substitutions maybe achieved by generating sequences in which the third position of oneor more selected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues. A “nucleic acid fragment” is a portion of a givennucleic acid molecule.

A “nucleotide sequence” is a polymer of DNA or RNA that can besingle-stranded or double-stranded, optionally containing synthetic,non-natural or altered nucleotide bases capable of incorporation intoDNA or RNA polymers.

The terms “nucleic acid,” “nucleic acid molecule,” “nucleic acidfragment,” “nucleic acid sequence or segment,” or “polynucleotide” areused interchangeably and may also be used interchangeably with gene,cDNA, DNA and RNA encoded by a gene.

The invention encompasses isolated or substantially purified nucleicacid nucleic acid molecules and compositions containing those molecules.In the context of the present invention, an “isolated” or “purified” DNAmolecule or RNA molecule is a DNA molecule or RNA molecule that existsapart from its native environment and is therefore not a product ofnature. An isolated DNA molecule or RNA molecule may exist in a purifiedform or may exist in a non-native environment such as, for example, atransgenic host cell. For example, an “isolated” or “purified” nucleicacid molecule or biologically active portion thereof, is substantiallyfree of other cellular material, or culture medium when produced byrecombinant techniques, or substantially free of chemical precursors orother chemicals when chemically synthesized. In one embodiment, an“isolated” nucleic acid is free of sequences that naturally flank thenucleic acid (i.e., sequences located at the 5′ and 3′ ends of thenucleic acid) in the genomic DNA of the organism from which the nucleicacid is derived. For example, in various embodiments, the isolatednucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flankthe nucleic acid molecule in genomic DNA of the cell from which thenucleic acid is derived. Fragments and variants of the disclosednucleotide sequences are also encompassed by the present invention. By“fragment” or “portion” is meant a full length or less than full lengthof the nucleotide sequence.

“Naturally occurring,” “native,” or “wild-type” is used to describe anobject that can be found in nature as distinct from being artificiallyproduced. For example, a protein or nucleotide sequence present in anorganism (including a virus), which can be isolated from a source innature and that has not been intentionally modified by a person in thelaboratory, is naturally occurring.

A “variant” of a molecule is a sequence that is substantially similar tothe sequence of the native molecule. For nucleotide sequences, variantsinclude those sequences that, because of the degeneracy of the geneticcode, encode the identical amino acid sequence of the native protein.Naturally occurring allelic variants such as these can be identifiedwith the use of molecular biology techniques, as, for example, withpolymerase chain reaction (PCR) and hybridization techniques. Variantnucleotide sequences also include synthetically derived nucleotidesequences, such as those generated, for example, by using site-directedmutagenesis, which encode the native protein, as well as those thatencode a polypeptide having amino acid substitutions. Generally,nucleotide sequence variants of the invention will have at least 40%,50%, 60%, to 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, to 79%,generally at least 80%, e.g., 81%-84%, at least 85%, e.g., 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, to 98%, sequenceidentity to the native (endogenous) nucleotide sequence.

The term “chimeric” refers to a gene or DNA that contains 1) DNAsequences, including regulatory and coding sequences that are not foundtogether in nature or 2) sequences encoding parts of proteins notnaturally adjoined, or 3) parts of promoters that are not naturallyadjoined. Accordingly, a chimeric gene may include regulatory sequencesand coding sequences that are derived from different sources, or includeregulatory sequences and coding sequences derived from the same source,but arranged in a manner different from that found in nature.

A “transgene” refers to a gene that has been introduced into the genomeby transformation. Transgenes include, for example, DNA that is eitherheterologous or homologous to the DNA of a particular cell to betransformed. Additionally, transgenes may include native genes insertedinto a non-native organism, or chimeric genes.

The term “endogenous gene” refers to a native gene in its naturallocation in the genome of an organism.

A “foreign” gene refers to a gene not normally found in the hostorganism that has been introduced by gene transfer.

The terms “protein,” “peptide” and “polypeptide” are usedinterchangeably herein.

“Conservatively modified variations” of a particular nucleic acidsequence refer to those nucleic acid sequences that encode identical oressentially identical amino acid sequences. Because of the degeneracy ofthe genetic code, a large number of functionally identical nucleic acidsencode any given polypeptide. For instance, the codons CGT, CGC, CGA,CGG, AGA and AGG all encode the amino acid arginine. Thus, at everyposition where an arginine is specified by a codon, the codon can bealtered to any of the corresponding codons described without alteringthe encoded protein. Such nucleic acid variations are “silentvariations,” which are one species of “conservatively modifiedvariations.” Every nucleic acid sequence described herein that encodes apolypeptide also describes every possible silent variation, except whereotherwise noted. One of skill in the art will recognize that each codonin a nucleic acid (except ATG, which is ordinarily the only codon formethionine) can be modified to yield a functionally identical moleculeby standard techniques. Accordingly, each “silent variation” of anucleic acid that encodes a polypeptide is implicit in each describedsequence.

“Recombinant DNA molecule” is a combination of DNA sequences that arejoined together using recombinant DNA technology and procedures used tojoin together DNA sequences as described, for example, in Sambrook andRussell (2001).

The terms “heterologous gene”, “heterologous DNA sequence”, “exogenousDNA sequence”, “heterologous RNA sequence”, “exogenous RNA sequence” or“heterologous nucleic acid” each refer to a sequence that eitheroriginates from a source foreign to the particular host cell, or is fromthe same source but is modified from its original or native form. Thus,a heterologous gene in a host cell includes a gene that is endogenous tothe particular host cell but has been modified through, for example, theuse of DNA shuffling. The terms also include non-naturally occurringmultiple copies of a naturally occurring DNA or RNA sequence. Thus, theterms refer to a DNA or RNA segment that is foreign or heterologous tothe cell, or homologous to the cell but in a position within the hostcell nucleic acid in which the element is not ordinarily found.Exogenous DNA segments are expressed to yield exogenous polypeptides.

A “homologous” DNA or RNA sequence is a sequence that is naturallyassociated with a host cell into which it is introduced.

“Wild-type” refers to the normal gene or organism found in nature.

“Genome” refers to the complete genetic material of an organism.

A “vector” is defined to include, inter alia, any viral vector, as wellas any plasmid, cosmid, phage or binary vector in double or singlestranded linear or circular form that may or may not be selftransmissible or mobilizable, and that can transform prokaryotic oreukaryotic host either by integration into the cellular genome or existextrachromosomally (e.g., autonomous replicating plasmid with an originof replication).

“Expression cassette” as used herein means a nucleic acid sequencecapable of directing expression of a particular nucleotide sequence inan appropriate host cell, which may include a promoter operably linkedto the nucleotide sequence of interest that may be operably linked totermination signals. The coding region usually codes for a functionalRNA of interest, for example an siRNA. The expression cassette includingthe nucleotide sequence of interest may be chimeric. The expressioncassette may also be one that is naturally occurring but has beenobtained in a recombinant form useful for heterologous expression. Theexpression of the nucleotide sequence in the expression cassette may beunder the control of a constitutive promoter or of a regulatablepromoter that initiates transcription only when the host cell is exposedto some particular stimulus. In the case of a multicellular organism,the promoter can also be specific to a particular tissue or organ orstage of development.

Such expression cassettes can include a transcriptional initiationregion linked to a nucleotide sequence of interest. Such an expressioncassette is provided with a plurality of restriction sites for insertionof the gene of interest to be under the transcriptional regulation ofthe regulatory regions. The expression cassette may additionally containselectable marker genes.

“Coding sequence” refers to a DNA or RNA sequence that codes for aspecific amino acid sequence. It may constitute an “uninterrupted codingsequence”, i.e., lacking an intron, such as in a cDNA, or it may includeone or more introns bounded by appropriate splice junctions. An “intron”is a sequence of RNA that is contained in the primary transcript but isremoved through cleavage and re-ligation of the RNA within the cell tocreate the mature mRNA that can be translated into a protein.

The term “open reading frame” (ORF) refers to the sequence betweentranslation initiation and termination codons of a coding sequence. Theterms “initiation codon” and “termination codon” refer to a unit ofthree adjacent nucleotides (a ‘codon’) in a coding sequence thatspecifies initiation and chain termination, respectively, of proteinsynthesis (mRNA translation).

“Functional RNA” refers to sense RNA, antisense RNA, ribozyme RNA,siRNA, or other RNA that may not be translated but yet has an effect onat least one cellular process.

The term “RNA transcript” or “transcript” refers to the productresulting from RNA polymerase catalyzed transcription of a DNA sequence.When the RNA transcript is a perfect complementary copy of the DNAsequence, it is referred to as the primary transcript or it may be a RNAsequence derived from posttranscriptional processing of the primarytranscript and is referred to as the mature RNA. “Messenger RNA” (mRNA)refers to the RNA that is without introns and that can be translatedinto protein by the cell.

“cDNA” refers to a single- or a double-stranded DNA that iscomplementary to and derived from mRNA.

“Regulatory sequences” are nucleotide sequences located upstream (5′non-coding sequences), within, or downstream (3′ non-coding sequences)of a coding sequence, and which influence the transcription, RNAprocessing or stability, or translation of the associated codingsequence. Regulatory sequences include enhancers, promoters, translationleader sequences, introns, and polyadenylation signal sequences. Theyinclude natural and synthetic sequences as well as sequences that may bea combination of synthetic and natural sequences. As is noted herein,the term “suitable regulatory sequences” is not limited to promoters.However, some suitable regulatory sequences useful in the presentinvention will include, but are not limited to constitutive promoters,tissue-specific promoters, development-specific promoters, regulatablepromoters and viral promoters.

“5′ non-coding sequence” refers to a nucleotide sequence located 5′(upstream) to the coding sequence. It is present in the fully processedmRNA upstream of the initiation codon and may affect processing of theprimary transcript to mRNA, mRNA stability or translation efficiency.

“3′ non-coding sequence” refers to nucleotide sequences located 3′(downstream) to a coding sequence and may include polyadenylation signalsequences and other sequences encoding regulatory signals capable ofaffecting mRNA processing or gene expression. The polyadenylation signalis usually characterized by affecting the addition of polyadenylic acidtracts to the 3′ end of the mRNA precursor.

The term “translation leader sequence” refers to that DNA sequenceportion of a gene between the promoter and coding sequence that istranscribed into RNA and is present in the fully processed mRNA upstream(5′) of the translation start codon. The translation leader sequence mayaffect processing of the primary transcript to mRNA, mRNA stability ortranslation efficiency.

The term “mature” protein refers to a post-translationally processedpolypeptide without its signal peptide. “Precursor” protein refers tothe primary product of translation of an mRNA. “Signal peptide” refersto the amino terminal extension of a polypeptide, which is translated inconjunction with the polypeptide forming a precursor peptide and whichis required for its entrance into the secretory pathway. The term“signal sequence” refers to a nucleotide sequence that encodes thesignal peptide.

“Promoter” refers to a nucleotide sequence, usually upstream (5′) to itscoding sequence, which directs and/or controls the expression of thecoding sequence by providing the recognition for RNA polymerase andother factors required for proper transcription. “Promoter” includes aminimal promoter that is a short DNA sequence comprised of a TATA-boxand other sequences that serve to specify the site of transcriptioninitiation, to which regulatory elements are added for control ofexpression. “Promoter” also refers to a nucleotide sequence thatincludes a minimal promoter plus regulatory elements that is capable ofcontrolling the expression of a coding sequence or functional RNA. Thistype of promoter sequence consists of proximal and more distal upstreamelements, the latter elements often referred to as enhancers.Accordingly, an “enhancer” is a DNA sequence that can stimulate promoteractivity and may be an innate element of the promoter or a heterologouselement inserted to enhance the level or tissue specificity of apromoter. It is capable of operating in both orientations (normal orflipped), and is capable of functioning even when moved either upstreamor downstream from the promoter. Both enhancers and other upstreampromoter elements bind sequence-specific DNA-binding proteins thatmediate their effects. Promoters may be derived in their entirety from anative gene, or be composed of different elements derived from differentpromoters found in nature, or even be comprised of synthetic DNAsegments. A promoter may also contain DNA sequences that are involved inthe binding of protein factors that control the effectiveness oftranscription initiation in response to physiological or developmentalconditions. Examples of promoters that may be used in the presentinvention include the mouse U6 RNA promoters, synthetic human H1RNApromoters, SV40, CMV, RSV, RNA polymerase II and RNA polymerase IIIpromoters.

The “initiation site” is the position surrounding the first nucleotidethat is part of the transcribed sequence, which is also defined asposition +1. With respect to this site all other sequences of the geneand its controlling regions are numbered. Downstream sequences (i.e.,further protein encoding sequences in the 3′ direction) are denominatedpositive, while upstream sequences (mostly of the controlling regions inthe 5′ direction) are denominated negative.

Promoter elements, particularly a TATA element, that are inactive orthat have greatly reduced promoter activity in the absence of upstreamactivation are referred to as “minimal or core promoters.” In thepresence of a suitable transcription factor, the minimal promoterfunctions to permit transcription. A “minimal or core promoter” thusconsists only of all basal elements needed for transcription initiation,e.g., a TATA box and/or an initiator.

“Constitutive expression” refers to expression using a constitutive orregulated promoter. “Conditional” and “regulated expression” refer toexpression controlled by a regulated promoter.

“Operably-linked” refers to the association of nucleic acid sequences onsingle nucleic acid fragment so that the function of one of thesequences is affected by another. For example, a regulatory DNA sequenceis said to be “operably linked to” or “associated with” a DNA sequencethat codes for an RNA or a polypeptide if the two sequences are situatedsuch that the regulatory DNA sequence affects expression of the codingDNA sequence (i.e., that the coding sequence or functional RNA is underthe transcriptional control of the promoter). Coding sequences can beoperably-linked to regulatory sequences in sense or antisenseorientation.

“Expression” refers to the transcription and/or translation of anendogenous gene, heterologous gene or nucleic acid segment, or atransgene in cells. For example, in the case of siRNA constructs,expression may refer to the transcription of the siRNA only. Inaddition, expression refers to the transcription and stable accumulationof sense (mRNA) or functional RNA. Expression may also refer to theproduction of protein.

“Altered levels” refers to the level of expression in transgenic cellsor organisms that differs from that of normal or untransformed cells ororganisms.

“Overexpression” refers to the level of expression in transgenic cellsor organisms that exceeds levels of expression in normal oruntransformed cells or organisms.

“Antisense inhibition” refers to the production of antisense RNAtranscripts capable of suppressing the expression of protein from anendogenous gene or a transgene.

“Transcription stop fragment” refers to nucleotide sequences thatcontain one or more regulatory signals, such as polyadenylation signalsequences, capable of terminating transcription. Examples include the 3′non-regulatory regions of genes encoding nopaline synthase and the smallsubunit of ribulose bisphosphate carboxylase.

“Translation stop fragment” refers to nucleotide sequences that containone or more regulatory signals, such as one or more termination codonsin all three frames, capable of terminating translation. Insertion of atranslation stop fragment adjacent to or near the initiation codon atthe 5′ end of the coding sequence will result in no translation orimproper translation. Excision of the translation stop fragment bysite-specific recombination will leave a site-specific sequence in thecoding sequence that does not interfere with proper translation usingthe initiation codon.

The terms “cis-acting sequence” and “cis-acting element” refer to DNA orRNA sequences whose functions require them to be on the same molecule.An example of a cis-acting sequence on the replicon is the viralreplication origin.

The terms “trans-acting sequence” and “trans-acting element” refer toDNA or RNA sequences whose function does not require them to be on thesame molecule.

“Chromosomally-integrated” refers to the integration of a foreign geneor nucleic acid construct into the host DNA by covalent bonds. Wheregenes are not “chromosomally integrated” they may be “transientlyexpressed.” Transient expression of a gene refers to the expression of agene that is not integrated into the host chromosome but functionsindependently, either as part of an autonomously replicating plasmid orexpression cassette, for example, or as part of another biologicalsystem such as a virus.

The following terms are used to describe the sequence relationshipsbetween two or more nucleic acids or polynucleotides: (a) “referencesequence,” (b) “comparison window,” (c) “sequence identity,” (d)“percentage of sequence identity,” and (e) “substantial identity.”

(a) As used herein, “reference sequence” is a defined sequence used as abasis for sequence comparison. A reference sequence may be a subset orthe entirety of a specified sequence; for example, as a segment of afull-length cDNA or gene sequence, or the complete cDNA or genesequence.

(b) As used herein, “comparison window” makes reference to a contiguousand specified segment of a polynucleotide sequence, wherein thepolynucleotide sequence in the comparison window may comprise additionsor deletions (i.e., gaps) compared to the reference sequence (which doesnot comprise additions or deletions) for optimal alignment of the twosequences. Generally, the comparison window is at least 20 contiguousnucleotides in length, and optionally can be 30, 40, 50, 100, or longer.Those of skill in the art understand that to avoid a high similarity toa reference sequence due to inclusion of gaps in the polynucleotidesequence a gap penalty is typically introduced and is subtracted fromthe number of matches.

Methods of alignment of sequences for comparison are well-known in theart. Thus, the determination of percent identity between any twosequences can be accomplished using a mathematical algorithm.

Computer implementations of these mathematical algorithms can beutilized for comparison of sequences to determine sequence identity.Such implementations include, but are not limited to: CLUSTAL in thePC/Gene program (available from Intelligenetics, Mountain View, Calif.);the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, andTFASTA in the Wisconsin Genetics Software Package, Version 8 (availablefrom Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis.,USA). Alignments using these programs can be performed using the defaultparameters.

Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information. This algorithm involvesfirst identifying high scoring sequence pairs (HSPs) by identifyingshort words of length W in the query sequence, which either match orsatisfy some positive-valued threshold score T when aligned with a wordof the same length in a database sequence. T is referred to as theneighborhood word score threshold. These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when thecumulative alignment score falls off by the quantity X from its maximumachieved value, the cumulative score goes to zero or below due to theaccumulation of one or more negative-scoring residue alignments, or theend of either sequence is reached.

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences. One measure of similarity provided by the BLAST algorithmis the smallest sum probability (P(N)), which provides an indication ofthe probability by which a match between two nucleotide sequences wouldoccur by chance. For example, a test nucleic acid sequence is consideredsimilar to a reference sequence if the smallest sum probability in acomparison of the test nucleic acid sequence to the reference nucleicacid sequence is less than about 0.1, more preferably less than about0.01, and most preferably less than about 0.001.

To obtain gapped alignments for comparison purposes, Gapped BLAST (inBLAST 2.0) can be utilized. Alternatively, PSI-BLAST (in BLAST 2.0) canbe used to perform an iterated search that detects distant relationshipsbetween molecules. When utilizing BLAST, Gapped BLAST, PSI-BLAST, thedefault parameters of the respective programs (e.g. BLASTN fornucleotide sequences) can be used. The BLASTN program (for nucleotidesequences) uses as defaults a wordlength (W) of 11, an expectation (E)of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands.Alignment may also be performed manually by inspection.

For purposes of the present invention, comparison of nucleotidesequences for determination of percent sequence identity to the promotersequences disclosed herein is preferably made using the BlastN program(version 1.4.7 or later) with its default parameters or any equivalentprogram. By “equivalent program” is intended any sequence comparisonprogram that, for any two sequences in question, generates an alignmenthaving identical nucleotide matches and an identical percent sequenceidentity when compared to the corresponding alignment generated by thepreferred program.

(c) As used herein, “sequence identity” or “identity” in the context oftwo nucleic acid sequences makes reference to a specified percentage ofnucleotides in the two sequences that are the same when aligned formaximum correspondence over a specified comparison window, as measuredby sequence comparison algorithms or by visual inspection.

(d) As used herein, “percentage of sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison, and multiplying the result by 100 to yield the percentage ofsequence identity.

(e) The term “substantial identity” of polynucleotide sequences meansthat a polynucleotide comprises a sequence that has at least 70%, 71%,72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably at least 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%,91%, 92%, 93%, or 94%, and most preferably at least 95%, 96%, 97%, 98%,or 99% sequence identity, compared to a reference sequence using one ofthe alignment programs described using standard parameters.

Another indication that nucleotide sequences are substantially identicalis if two molecules hybridize to each other under stringent conditions.Generally, stringent conditions are selected to be about 5° C. lowerthan the thermal melting point (Tm) for the specific sequence at adefined ionic strength and pH. However, stringent conditions encompasstemperatures in the range of about 1° C. to about 20° C., depending uponthe desired degree of stringency as otherwise qualified herein.

For sequence comparison, typically one sequence acts as a referencesequence to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are input into acomputer, subsequence coordinates are designated if necessary, andsequence algorithm program parameters are designated. The sequencecomparison algorithm then calculates the percent sequence identity forthe test sequence(s) relative to the reference sequence, based on thedesignated program parameters.

As noted herein, another indication that two nucleic acid sequences aresubstantially identical is that the two molecules hybridize to eachother under stringent conditions. The phrase “hybridizing specificallyto” refers to the binding, duplexing, or hybridizing of a molecule onlyto a particular nucleotide sequence under stringent conditions when thatsequence is present in a complex mixture (e.g., total cellular) DNA orRNA. “Bind(s) substantially” refers to complementary hybridizationbetween a probe nucleic acid and a target nucleic acid and embracesminor mismatches that can be accommodated by reducing the stringency ofthe hybridization media to achieve the desired detection of the targetnucleic acid sequence.

“Stringent hybridization conditions” and “stringent hybridization washconditions” in the context of nucleic acid hybridization experimentssuch as Southern and Northern hybridizations are sequence dependent, andare different under different environmental parameters. Longer sequenceshybridize specifically at higher temperatures. The Tm is the temperature(under defined ionic strength and pH) at which 50% of the targetsequence hybridizes to a perfectly matched probe. Specificity istypically the function of post-hybridization washes, the criticalfactors being the ionic strength and temperature of the final washsolution. For DNA-DNA hybrids, the Tm can be approximated from theequation of Meinkoth and Wahl (1984); Tm 81.5° C.+16.6 (log M)+0.41 (%GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations,% GC is the percentage of guanosine and cytosine nucleotides in the DNA,% form is the percentage of formamide in the hybridization solution, andL is the length of the hybrid in base pairs. Tm is reduced by about 1°C. for each 1% of mismatching; thus, Tm, hybridization, and/or washconditions can be adjusted to hybridize to sequences of the desiredidentity. For example, if sequences with >90% identity are sought, theTm can be decreased 10° C. Generally, stringent conditions are selectedto be about 5° C. lower than the thermal melting point (Tm) for thespecific sequence and its complement at a defined ionic strength and pH.However, severely stringent conditions can utilize a hybridizationand/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point(Tm); moderately stringent conditions can utilize a hybridization and/orwash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm);low stringency conditions can utilize a hybridization and/or wash at 11,12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm).Using the equation, hybridization and wash compositions, and desired T,those of ordinary skill will understand that variations in thestringency of hybridization and/or wash solutions are inherentlydescribed. If the desired degree of mismatching results in a T of lessthan 45° C. (aqueous solution) or 32° C. (formamide solution), it ispreferred to increase the SSC concentration so that a higher temperaturecan be used. Generally, highly stringent hybridization and washconditions are selected to be about 5° C. lower than the thermal meltingpoint (Tm) for the specific sequence at a defined ionic strength and pH.

An example of highly stringent wash conditions is 0.15 M NaCl at 72° C.for about 15 minutes. An example of stringent wash conditions is a0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook and Russell 2001,for a description of SSC buffer). Often, a high stringency wash ispreceded by a low stringency wash to remove background probe signal. Forshort nucleic acid sequences (e.g., about 10 to 50 nucleotides),stringent conditions typically involve salt concentrations of less thanabout 1.5 M, more preferably about 0.01 to 1.0 M, Na ion concentration(or other salts) at pH 7.0 to 8.3, and the temperature is typically atleast about 30° C. Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. In general, a signalto noise ratio of 2× (or higher) than that observed for an unrelatedprobe in the particular hybridization assay indicates detection of aspecific hybridization. Very stringent conditions are selected to beequal to the Tm for a particular nucleic acid molecule.

Very stringent conditions are selected to be equal to the Tm for aparticular probe. An example of stringent conditions for hybridizationof complementary nucleic acids which have more than 100 complementaryresidues on a filter in a Southern or Northern blot is 50% formamide,e.g., hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and awash in 0.1×SSC at 60 to 65° C. Exemplary low stringency conditionsinclude hybridization with a buffer solution of 30 to 35% formamide, 1MNaCl, 1% SDS (sodium dodecyl sulfate) at 37° C., and a wash in 1× to2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C.Exemplary moderate stringency conditions include hybridization in 40 to45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSCat 55 to 60° C.

The term “transformation” refers to the transfer of a nucleic acidfragment into the genome of a host cell, resulting in genetically stableinheritance. A “host cell” is a cell that has been transformed, or iscapable of transformation, by an exogenous nucleic acid molecule. Hostcells containing the transformed nucleic acid fragments are referred toas “transgenic” cells.

“Transformed,” “transduced,” “transgenic” and “recombinant” refer to ahost cell into which a heterologous nucleic acid molecule has beenintroduced. As used herein the term “transfection” refers to thedelivery of DNA into eukaryotic (e.g., mammalian) cells. The term“transformation” is used herein to refer to delivery of DNA intoprokaryotic (e.g., E. coli) cells. The term “transduction” is usedherein to refer to infecting cells with viral particles. The nucleicacid molecule can be stably integrated into the genome generally knownin the art. Known methods of PCR include, but are not limited to,methods using paired primers, nested primers, single specific primers,degenerate primers, gene-specific primers, vector-specific primers,partially mismatched primers, and the like. For example, “transformed,”“transformant,” and “transgenic” cells have been through thetransformation process and contain a foreign gene integrated into theirchromosome. The term “untransformed” refers to normal cells that havenot been through the transformation process.

“Genetically altered cells” denotes cells which have been modified bythe introduction of recombinant or heterologous nucleic acids (e.g., oneor more DNA constructs or their RNA counterparts) and further includesthe progeny of such cells which retain part or all of such geneticmodification.

As used herein, the term “derived” or “directed to” with respect to anucleotide molecule means that the molecule has complementary sequenceidentity to a particular molecule of interest.

The siRNAs of the present invention can be generated by any method knownto the art, for example, by in vitro transcription, recombinantly, or bysynthetic means. In one example, the siRNAs can be generated in vitro byusing a recombinant enzyme, such as T7 RNA polymerase, and DNAoligonucleotide templates.

II. Nucleic Acid Molecules of the Invention

The terms “isolated and/or purified” refer to in vitro isolation of anucleic acid, e.g., a DNA or RNA molecule from its natural cellularenvironment, and from association with other components of the cell,such as nucleic acid or polypeptide, so that it can be sequenced,replicated, and/or expressed. The RNA or DNA is “isolated” in that it isfree from at least one contaminating nucleic acid with which it isnormally associated in the natural source of the RNA or DNA and ispreferably substantially free of any other mammalian RNA or DNA. Thephrase “free from at least one contaminating source nucleic acid withwhich it is normally associated” includes the case where the nucleicacid is reintroduced into the source or natural cell but is in adifferent chromosomal location or is otherwise flanked by nucleic acidsequences not normally found in the source cell, e.g., in a vector orplasmid.

In addition to a DNA sequence encoding a siRNA, the nucleic acidmolecules of the invention include double-stranded interfering RNAmolecules, which are also useful to inhibit expression of a target gene.

As used herein, the term “recombinant nucleic acid”, e.g., “recombinantDNA sequence or segment” refers to a nucleic acid, e.g., to DNA, thathas been derived or isolated from any appropriate cellular source, thatmay be subsequently chemically altered in vitro, so that its sequence isnot naturally occurring, or corresponds to naturally occurring sequencesthat are not positioned as they would be positioned in a genome whichhas not been transformed with exogenous DNA. An example of preselectedDNA “derived” from a source would be a DNA sequence that is identifiedas a useful fragment within a given organism, and which is thenchemically synthesized in essentially pure form. An example of such DNA“isolated” from a source would be a useful DNA sequence that is excisedor removed from said source by chemical means, e.g., by the use ofrestriction endonucleases, so that it can be further manipulated, e.g.,amplified, for use in the invention, by the methodology of geneticengineering.

Thus, recovery or isolation of a given fragment of DNA from arestriction digest can employ separation of the digest on polyacrylamideor agarose gel by electrophoresis, identification of the fragment ofinterest by comparison of its mobility versus that of marker DNAfragments of known molecular weight, removal of the gel sectioncontaining the desired fragment, and separation of the gel from DNA.Therefore, “recombinant DNA” includes completely synthetic DNAsequences, semi-synthetic DNA sequences, DNA sequences isolated frombiological sources, and DNA sequences derived from RNA, as well asmixtures thereof.

Nucleic acid molecules having base substitutions (i.e., variants) areprepared by a variety of methods known in the art. These methodsinclude, but are not limited to, isolation from a natural source (in thecase of naturally occurring sequence variants) or preparation byoligonucleotide-mediated (or site-directed) mutagenesis, PCRmutagenesis, and cassette mutagenesis of an earlier prepared variant ora non-variant version of the nucleic acid molecule.

Oligonucleotide-mediated mutagenesis is a method for preparingsubstitution variants. This technique is known in the art. Briefly,nucleic acid encoding a siRNA can be altered by hybridizing anoligonucleotide encoding the desired mutation to a DNA template, wherethe template is the single-stranded form of a plasmid or bacteriophagecontaining the unaltered or native gene sequence. After hybridization, aDNA polymerase is used to synthesize an entire second complementarystrand of the template that will thus incorporate the oligonucleotideprimer, and will code for the selected alteration in the nucleic acidencoding siRNA. The oligonucleotides are readily synthesized usingtechniques known in the art.

The DNA template can be generated by those vectors that are eitherderived from bacteriophage M13 vectors (the commercially available M13mp18 and M13 mp19 vectors are suitable), or those vectors that contain asingle-stranded phage origin of replication. Thus, the DNA that is to bemutated may be inserted into one of these vectors to generatesingle-stranded template. Production of the single-stranded template isdescribed in Chapter 3 of Sambrook and Russell, 2001. Alternatively,single-stranded DNA template may be generated by denaturingdouble-stranded plasmid (or other) DNA using standard techniques.

For alteration of the native DNA sequence (to generate amino acidsequence variants, for example), the oligonucleotide is hybridized tothe single-stranded template under suitable hybridization conditions. ADNA polymerizing enzyme, usually the Klenow fragment of DNA polymeraseI, is then added to synthesize the complementary strand of the templateusing the oligonucleotide as a primer for synthesis. A heteroduplexmolecule is thus formed such that one strand of DNA encodes the mutatedform of the DNA, and the other strand (the original template) encodesthe native, unaltered sequence of the DNA. This heteroduplex molecule isthen transformed into a suitable host cell, usually a prokaryote such asE. coli JM101. After the cells are grown, they are plated onto agaroseplates and screened using the oligonucleotide primer radiolabeled with32-phosphate to identify the bacterial colonies that contain the mutatedDNA. The mutated region is then removed and placed in an appropriatevector, generally an expression vector of the type typically employedfor transformation of an appropriate host.

The method described immediately above may be modified such that ahomoduplex molecule is created wherein both strands of the plasmidcontain the mutations(s). The modifications are as follows: Thesingle-stranded oligonucleotide is annealed to the single-strandedtemplate as described herein. A mixture of three deoxyribonucleotides,deoxyriboadenosine (dATP), deoxyriboguanosine (dGTP), anddeoxyribothymidine (dTTP), is combined with a modifiedthiodeoxyribocytosine called dCTP-(*S) (which can be obtained from theAmersham Corporation). This mixture is added to thetemplate-oligonucleotide complex. Upon addition of DNA polymerase tothis mixture, a strand of DNA identical to the template except for themutated bases is generated. In addition, this new strand of DNA willcontain dCTP-(*S) instead of dCTP, which serves to protect it fromrestriction endonuclease digestion.

After the template strand of the double-stranded heteroduplex is nickedwith an appropriate restriction enzyme, the template strand can bedigested with ExoIII nuclease or another appropriate nuclease past theregion that contains the site(s) to be mutagenized. The reaction is thenstopped to leave a molecule that is only partially single-stranded. Acomplete double-stranded DNA homoduplex is then formed using DNApolymerase in the presence of all four deoxyribonucleotidetriphosphates, ATP, and DNA ligase. This homoduplex molecule can then betransformed into a suitable host cell such as E. coli JM101.

III. Expression Cassettes of the Invention

To prepare expression cassettes, the recombinant DNA sequence or segmentmay be circular or linear, double-stranded or single-stranded.Generally, the DNA sequence or segment is in the form of chimeric DNA,such as plasmid DNA or a vector that can also contain coding regionsflanked by control sequences that promote the expression of therecombinant DNA present in the resultant transformed cell.

A “chimeric” vector or expression cassette, as used herein, means avector or cassette including nucleic acid sequences from at least twodifferent species, or has a nucleic acid sequence from the same speciesthat is linked or associated in a manner that does not occur in the“native” or wild type of the species.

Aside from recombinant DNA sequences that serve as transcription unitsfor an RNA transcript, or portions thereof, a portion of the recombinantDNA may be untranscribed, serving a regulatory or a structural function.For example, the recombinant DNA may have a promoter that is active inmammalian cells.

Other elements functional in the host cells, such as introns, enhancers,polyadenylation sequences and the like, may also be a part of therecombinant DNA. Such elements may or may not be necessary for thefunction of the DNA, but may provide improved expression of the DNA byaffecting transcription, stability of the siRNA, or the like. Suchelements may be included in the DNA as desired to obtain the optimalperformance of the siRNA in the cell.

Control sequences are DNA sequences necessary for the expression of anoperably linked coding sequence in a particular host organism. Thecontrol sequences that are suitable for prokaryotic cells, for example,include a promoter, and optionally an operator sequence, and a ribosomebinding site. Eukaryotic cells are known to utilize promoters,polyadenylation signals, and enhancers.

Operably linked nucleic acids are nucleic acids placed in a functionalrelationship with another nucleic acid sequence. For example, a promoteror enhancer is operably linked to a coding sequence if it affects thetranscription of the sequence; or a ribosome binding site is operablylinked to a coding sequence if it is positioned so as to facilitatetranslation. Generally, operably linked DNA sequences are DNA sequencesthat are linked are contiguous. However, enhancers do not have to becontiguous. Linking is accomplished by ligation at convenientrestriction sites. If such sites do not exist, the syntheticoligonucleotide adaptors or linkers are used in accord with conventionalpractice.

The recombinant DNA to be introduced into the cells may contain either aselectable marker gene or a reporter gene or both to facilitateidentification and selection of expressing cells from the population ofcells sought to be transfected or infected through viral vectors. Inother embodiments, the selectable marker may be carried on a separatepiece of DNA and used in a co-transfection procedure. Both selectablemarkers and reporter genes may be flanked with appropriate regulatorysequences to enable expression in the host cells. Useful selectablemarkers are known in the art and include, for example,antibiotic-resistance genes, such as neo and the like.

Reporter genes are used for identifying potentially transfected cellsand for evaluating the functionality of regulatory sequences. Reportergenes that encode for easily assayable proteins are well known in theart. In general, a reporter gene is a gene that is not present in orexpressed by the recipient organism or tissue and that encodes a proteinwhose expression is manifested by some easily detectable property, e.g.,enzymatic activity. For example, reporter genes include thechloramphenicol acetyl transferase gene (cat) from Tn9 of E. coli andthe luciferase gene from firefly Photinus pyralis. Expression of thereporter gene is assayed at a suitable time after the DNA has beenintroduced into the recipient cells.

The general methods for constructing recombinant DNA that can transfecttarget cells are well known to those skilled in the art, and the samecompositions and methods of construction may be utilized to produce theDNA useful herein.

The recombinant DNA can be readily introduced into the host cells, e.g.,mammalian, bacterial, yeast or insect cells by transfection with anexpression vector composed of DNA encoding the siRNA by any procedureuseful for the introduction into a particular cell, e.g., physical orbiological methods, to yield a cell having the recombinant DNA stablyintegrated into its genome or existing as a episomal element, so thatthe DNA molecules, or sequences of the present invention are expressedby the host cell. Preferably, the DNA is introduced into host cells viaa vector. The host cell is preferably of eukaryotic origin, e.g., plant,mammalian, insect, yeast or fungal sources, but host cells ofnon-eukaryotic origin may also be employed.

Physical methods to introduce a preselected DNA into a host cell includecalcium phosphate precipitation, lipofection, particle bombardment,microinjection, electroporation, and the like. Biological methods tointroduce the DNA of interest into a host cell include the use of DNAand RNA viral vectors. For mammalian gene therapy, as described hereinbelow, it is desirable to use an efficient means of inserting a copygene into the host genome. Viral vectors, and especially retroviralvectors, have become the most widely used method for inserting genesinto mammalian, e.g., human cells. Other viral vectors can be derivedfrom poxviruses, herpes simplex virus I, adenoviruses andadeno-associated viruses, and the like. See, for example, U.S. Pat. Nos.5,350,674 and 5,585,362.

As discussed herein, a “transfected”, “or “transduced” host cell or cellline is one in which the genome has been altered or augmented by thepresence of at least one heterologous or recombinant nucleic acidsequence. The host cells of the present invention are typically producedby transfection with a DNA sequence in a plasmid expression vector, aviral expression vector, or as an isolated linear DNA sequence. Thetransfected DNA can become a chromosomally integrated recombinant DNAsequence, which is composed of sequence encoding the siRNA.

To confirm the presence of the recombinant DNA sequence in the hostcell, a variety of assays may be performed. Such assays include, forexample, “molecular biological” assays well known to those of skill inthe art, such as Southern and Northern blotting, RT-PCR and PCR;“biochemical” assays, such as detecting the presence or absence of aparticular peptide, e.g., by immunological means (ELISAs and Westernblots) or by assays described herein to identify agents falling withinthe scope of the invention.

To detect and quantitate RNA produced from introduced recombinant DNAsegments, RT-PCR may be employed. In this application of PCR, it isfirst necessary to reverse transcribe RNA into DNA, using enzymes suchas reverse transcriptase, and then through the use of conventional PCRtechniques amplify the DNA. In most instances PCR techniques, whileuseful, will not demonstrate integrity of the RNA product. Furtherinformation about the nature of the RNA product may be obtained byNorthern blotting. This technique demonstrates the presence of an RNAspecies and gives information about the integrity of that RNA. Thepresence or absence of an RNA species can also be determined using dotor slot blot Northern hybridizations. These techniques are modificationsof Northern blotting and only demonstrate the presence or absence of anRNA species.

While Southern blotting and PCR may be used to detect the recombinantDNA segment in question, they do not provide information as to whetherthe preselected DNA segment is being expressed. Expression may beevaluated by specifically identifying the peptide products of theintroduced recombinant DNA sequences or evaluating the phenotypicchanges brought about by the expression of the introduced recombinantDNA segment in the host cell.

The instant invention provides a cell expression system for expressingexogenous nucleic acid material in a mammalian recipient. The expressionsystem, also referred to as a “genetically modified cell,” comprises acell and an expression vector for expressing the exogenous nucleic acidmaterial. The genetically modified cells are suitable for administrationto a mammalian recipient, where they replace the endogenous cells of therecipient. Thus, the preferred genetically modified cells arenon-immortalized and are non-tumorigenic.

According to one embodiment, the cells are transfected or otherwisegenetically modified ex vivo. The cells are isolated from a mammal(preferably a human), nucleic acid introduced (i.e., transduced ortransfected in vitro) with a vector for expressing a heterologous (e.g.,recombinant) gene encoding the therapeutic agent, and then administeredto a mammalian recipient for delivery of the therapeutic agent in situ.The mammalian recipient may be a human and the cells to be modified areautologous cells, i.e., the cells are isolated from the mammalianrecipient.

According to another embodiment, the cells are transfected or transducedor otherwise genetically modified in vivo. The cells from the mammalianrecipient are transduced or transfected in vivo with a vector containingexogenous nucleic acid material for expressing a heterologous (e.g.,recombinant) gene encoding a therapeutic agent and the therapeutic agentis delivered in situ.

As used herein, “exogenous nucleic acid material” refers to a nucleicacid or an oligonucleotide, either natural or synthetic, which is notnaturally found in the cells; or if it is naturally found in the cells,is modified from its original or native form. Thus, “exogenous nucleicacid material” includes, for example, a non-naturally occurring nucleicacid that can be transcribed into an anti-sense RNA, a siRNA, as well asa “heterologous gene” (i.e., a gene encoding a protein that is notexpressed or is expressed at biologically insignificant levels in anaturally-occurring cell of the same type). To illustrate, a syntheticor natural gene encoding human erythropoietin (EPO) would be considered“exogenous nucleic acid material” with respect to human peritonealmesothelial cells since the latter cells do not naturally express EPO.Still another example of “exogenous nucleic acid material” is theintroduction of only part of a gene to create a recombinant gene, suchas combining an regulatable promoter with an endogenous coding sequencevia homologous recombination.

The condition amenable to gene inhibition therapy may be a prophylacticprocess, i.e., a process for preventing disease or an undesired medicalcondition. Thus, the instant invention embraces a system for deliveringsiRNA that has a prophylactic function (i.e., a prophylactic agent) tothe mammalian recipient.

IV. Methods for Introducing the Expression Cassettes of the Inventioninto Cells

The inhibitory nucleic acid material (e.g., an expression cassetteencoding siRNA directed to a gene of interest) can be introduced intothe cell ex vivo or in vivo by genetic transfer methods, such astransfection or transduction, to provide a genetically modified cell.Various expression vectors (i.e., vehicles for facilitating delivery ofexogenous nucleic acid into a target cell) are known to one of ordinaryskill in the art.

As used herein, “transfection of cells” refers to the acquisition by acell of new nucleic acid material by incorporation of added DNA. Thus,transfection refers to the insertion of nucleic acid into a cell usingphysical or chemical methods. Several transfection techniques are knownto those of ordinary skill in the art including calcium phosphate DNAco-precipitation, DEAE-dextran, electroporation, cationicliposome-mediated transfection, tungsten particle-facilitatedmicroparticle bombardment, and strontium phosphate DNA co-precipitation.

In contrast, “transduction of cells” refers to the process oftransferring nucleic acid into a cell using a DNA or RNA virus. A RNAvirus (i.e., a retrovirus) for transferring a nucleic acid into a cellis referred to herein as a transducing chimeric retrovirus. Exogenousnucleic acid material contained within the retrovirus is incorporatedinto the genome of the transduced cell. A cell that has been transducedwith a chimeric DNA virus (e.g., an adenovirus carrying a cDNA encodinga therapeutic agent), will not have the exogenous nucleic acid materialincorporated into its genome but will be capable of expressing theexogenous nucleic acid material that is retained extrachromosomallywithin the cell.

The exogenous nucleic acid material can include the nucleic acidencoding the siRNA together with a promoter to control transcription.The promoter characteristically has a specific nucleotide sequencenecessary to initiate transcription. The exogenous nucleic acid materialmay further include additional sequences (i.e., enhancers) required toobtain the desired gene transcription activity. For the purpose of thisdiscussion an “enhancer” is simply any non-translated DNA sequence thatworks with the coding sequence (in cis) to change the basaltranscription level dictated by the promoter. The exogenous nucleic acidmaterial may be introduced into the cell genome immediately downstreamfrom the promoter so that the promoter and coding sequence areoperatively linked so as to permit transcription of the coding sequence.An expression vector can include an exogenous promoter element tocontrol transcription of the inserted exogenous gene. Such exogenouspromoters include both constitutive and regulatable promoters.

Naturally-occurring constitutive promoters control the expression ofessential cell functions. As a result, a nucleic acid sequence under thecontrol of a constitutive promoter is expressed under all conditions ofcell growth. Constitutive promoters include the promoters for thefollowing genes which encode certain constitutive or “housekeeping”functions: hypoxanthine phosphoribosyl transferase (HPRT), dihydrofolatereductase (DHFR), adenosine deaminase, phosphoglycerol kinase (PGK),pyruvate kinase, phosphoglycerol mutase, the beta-actin promoter, andother constitutive promoters known to those of skill in the art. Inaddition, many viral promoters function constitutively in eukaryoticcells. These include: the early and late promoters of SV40; the longterminal repeats (LTRs) of Moloney Leukemia Virus and otherretroviruses; and the thymidine kinase promoter of Herpes Simplex Virus,among many others.

Nucleic acid sequences that are under the control of regulatablepromoters are expressed only or to a greater or lesser degree in thepresence of an inducing or repressing agent, (e.g., transcription undercontrol of the metallothionein promoter is greatly increased in presenceof certain metal ions). Regulatable promoters include responsiveelements (REs) that stimulate transcription when their inducing factorsare bound. For example, there are REs for serum factors, steroidhormones, retinoic acid, cyclic AMP, and tetracycline and doxycycline.Promoters containing a particular RE can be chosen in order to obtain anregulatable response and in some cases, the RE itself may be attached toa different promoter, thereby conferring regulatability to the encodednucleic acid sequence. Thus, by selecting the appropriate promoter(constitutive versus regulatable; strong versus weak), it is possible tocontrol both the existence and level of expression of a nucleic acidsequence in the genetically modified cell. If the nucleic acid sequenceis under the control of an regulatable promoter, delivery of thetherapeutic agent in situ is triggered by exposing the geneticallymodified cell in situ to conditions for permitting transcription of thenucleic acid sequence, e.g., by intraperitoneal injection of specificinducers of the regulatable promoters which control transcription of theagent. For example, in situ expression of a nucleic acid sequence underthe control of the metallothionein promoter in genetically modifiedcells is enhanced by contacting the genetically modified cells with asolution containing the appropriate (i.e., inducing) metal ions in situ.

Accordingly, the amount of siRNA generated in situ is regulated bycontrolling such factors as the nature of the promoter used to directtranscription of the nucleic acid sequence, (i.e., whether the promoteris constitutive or regulatable, strong or weak) and the number of copiesof the exogenous nucleic acid sequence encoding a siRNA sequence thatare in the cell.

In addition to at least one promoter and at least one heterologousnucleic acid sequence encoding the siRNA, the expression vector mayinclude a selection gene, for example, a neomycin resistance gene, forfacilitating selection of cells that have been transfected or transducedwith the expression vector.

Cells can also be transfected with two or more expression vectors, atleast one vector containing the nucleic acid sequence(s) encoding thesiRNA(s), the other vector containing a selection gene. The selection ofa suitable promoter, enhancer, selection gene, and/or signal sequence isdeemed to be within the scope of one of ordinary skill in the artwithout undue experimentation.

The following discussion is directed to various utilities of the instantinvention. For example, the instant invention has utility as anexpression system suitable for silencing the expression of gene(s) ofinterest.

The instant invention also provides methods for genetically modifyingcells of a mammalian recipient in vivo. According to one embodiment, themethod comprises introducing an expression vector for expressing a siRNAsequence in cells of the mammalian recipient in situ by, for example,injecting the vector into the recipient.

V. Delivery Vehicles for the Expression Cassettes of the Invention

Delivery of compounds into tissues and across the blood-brain barriercan be limited by the size and biochemical properties of the compounds.Currently, efficient delivery of compounds into cells in vivo can beachieved only when the molecules are small (usually less than 600Daltons). Gene transfer for the correction of inborn errors ofmetabolism and neurodegenerative diseases of the central nervous system(CNS), and for the treatment of cancer has been accomplished withrecombinant adenoviral vectors.

The selection and optimization of a particular expression vector forexpressing a specific siRNA in a cell can be accomplished by obtainingthe nucleic acid sequence of the siRNA, possibly with one or moreappropriate control regions (e.g., promoter, insertion sequence);preparing a vector construct comprising the vector into which isinserted the nucleic acid sequence encoding the siRNA; transfecting ortransducing cultured cells in vitro with the vector construct; anddetermining whether the siRNA is present in the cultured cells.

Vectors for cell gene therapy include viruses, such asreplication-deficient viruses (described in detail below). Exemplaryviral vectors are derived from Harvey Sarcoma virus, ROUS Sarcoma virus,(MPSV), Moloney murine leukemia virus and DNA viruses (e.g.,adenovirus).

Replication-deficient retroviruses are capable of directing synthesis ofall virion proteins, but are incapable of making infectious particles.Accordingly, these genetically altered retroviral expression vectorshave general utility for high-efficiency transduction of nucleic acidsequences in cultured cells, and specific utility for use in the methodof the present invention. Such retroviruses further have utility for theefficient transduction of nucleic acid sequences into cells in vivo.Retroviruses have been used extensively for transferring nucleic acidmaterial into cells. Protocols for producing replication-deficientretroviruses (including the steps of incorporation of exogenous nucleicacid material into a plasmid, transfection of a packaging cell line withplasmid, production of recombinant retroviruses by the packaging cellline, collection of viral particles from tissue culture media, andinfection of the target cells with the viral particles) are well knownin the art.

An advantage of using retroviruses for gene therapy is that the virusesinsert the nucleic acid sequence encoding the siRNA into the host cellgenome, thereby permitting the nucleic acid sequence encoding the siRNAto be passed on to the progeny of the cell when it divides. Promotersequences in the LTR region have can enhance expression of an insertedcoding sequence in a variety of cell types. Some disadvantages of usinga retrovirus expression vector are (1) insertional mutagenesis, i.e.,the insertion of the nucleic acid sequence encoding the siRNA into anundesirable position in the target cell genome which, for example, leadsto unregulated cell growth and (2) the need for target cellproliferation in order for the nucleic acid sequence encoding the siRNAcarried by the vector to be integrated into the target genome.

Another viral candidate useful as an expression vector fortransformation of cells is the adenovirus, a double-stranded DNA virus.The adenovirus is infective in a wide range of cell types, including,for example, muscle and endothelial cells.

Adenoviruses (Ad) are double-stranded linear DNA viruses with a 36 kbgenome. Several features of adenovirus have made them useful astransgene delivery vehicles for therapeutic applications, such asfacilitating in vivo gene delivery. Recombinant adenovirus vectors havebeen shown to be capable of efficient in situ gene transfer toparenchymal cells of various organs, including the lung, brain,pancreas, gallbladder, and liver. This has allowed the use of thesevectors in methods for treating inherited genetic diseases, such ascystic fibrosis, where vectors may be delivered to a target organ. Inaddition, the ability of the adenovirus vector to accomplish in situtumor transduction has allowed the development of a variety ofanticancer gene therapy methods for non-disseminated disease. In thesemethods, vector containment favors tumor cell-specific transduction.

Like the retrovirus, the adenovirus genome is adaptable for use as anexpression vector for gene therapy, i.e., by removing the geneticinformation that controls production of the virus itself. Because theadenovirus functions in an extrachromosomal fashion, the recombinantadenovirus does not have the theoretical problem of insertionalmutagenesis.

Several approaches traditionally have been used to generate therecombinant adenoviruses. One approach involves direct ligation ofrestriction endonuclease fragments containing a nucleic acid sequence ofinterest to portions of the adenoviral genome. Alternatively, thenucleic acid sequence of interest may be inserted into a defectiveadenovirus by homologous recombination results. The desired recombinantsare identified by screening individual plaques generated in a lawn ofcomplementation cells.

Most adenovirus vectors are based on the adenovirus type 5 (Ad5)backbone in which an expression cassette containing the nucleic acidsequence of interest has been introduced in place of the early region 1(E1) or early region 3 (E3). Viruses in which E1 has been deleted aredefective for replication and are propagated in human complementationcells (e.g., 293 or 911 cells), which supply the missing gene E1 and pIXin trans.

In one embodiment of the present invention, one will desire to generatesiRNA in a brain cell or brain tissue. A suitable vector for thisapplication is an FIV vector or an AAV vector. For example, one may useAAV5. Also, one may apply poliovirus or HSV vectors.

Application of siRNA is generally accomplished by transfection ofsynthetic siRNAs, in vitro synthesized RNAs, or plasmids expressingshRNAs or miRNAs. More recently, viruses have been employed for in vitrostudies and to generate transgenic mouse knock-downs of targeted genes.Recombinant adenovirus, adeno-associated virus (AAV) and felineimmunodeficiency virus (FIV) can be used to deliver genes in vitro andin vivo. Each has its own advantages and disadvantages. Adenoviruses aredouble stranded DNA viruses with large genomes (36 kb) and have beenengineered by my laboratory and others to accommodate expressioncassettes in distinct regions.

Adeno-associated viruses have encapsidated genomes, similar to Ad, butare smaller in size and packaging capacity (˜30 nm vs. ˜100 nm;packaging limit of 4.5 kb). AAV contain single stranded DNA genomes ofthe + or the − strand. Eight serotypes of AAV (1-8) have been studiedextensively, three of which have been evaluated in the brain. Animportant consideration for the present application is that AAV5transduces striatal and cortical neurons, and is not associated with anyknown pathologies.

Adeno associated virus (AAV) is a small nonpathogenic virus of theparvoviridae family. AAV is distinct from the other members of thisfamily by its dependence upon a helper virus for replication. In theabsence of a helper virus, AAV may integrate in a locus specific mannerinto the q arm of chromosome 19. The approximately 5 kb genome of AAVconsists of one segment of single stranded DNA of either plus or minuspolarity. The ends of the genome are short inverted terminal repeatswhich can fold into hairpin structures and serve as the origin of viralDNA replication. Physically, the parvovirus virion is non-enveloped andits icosohedral capsid is approximately 20 nm in diameter.

Further provided by this invention are chimeric viruses where AAV can becombined with herpes virus, herpes virus amplicons, baculovirus or otherviruses to achieve a desired tropism associated with another virus. Forexample, the AAV4 ITRs could be inserted in the herpes virus and cellscould be infected. Post-infection, the ITRs of AAV4 could be acted on byAAV4 rep provided in the system or in a separate vehicle to rescue AAV4from the genome. Therefore, the cellular tropism of the herpes simplexvirus can be combined with AAV4 rep mediated targeted integration. Otherviruses that could be utilized to construct chimeric viruses includelentivirus, retrovirus, pseudotyped retroviral vectors, and adenoviralvectors.

Also provided by this invention are variant AAV vectors. For example,the sequence of a native AAV, such as AAV5, can be modified atindividual nucleotides. The present invention includes native and mutantAAV vectors. The present invention further includes all AAV serotypes.

FIV is an enveloped virus with a strong safety profile in humans;individuals bitten or scratched by FIV-infected cats do not seroconvertand have not been reported to show any signs of disease. Like AAV, FIVprovides lasting transgene expression in mouse and nonhuman primateneurons, and transduction can be directed to different cell types bypseudotyping, the process of exchanging the virus's native envelope foran envelope from another virus.

Thus, as will be apparent to one of ordinary skill in the art, a varietyof suitable viral expression vectors are available for transferringexogenous nucleic acid material into cells. The selection of anappropriate expression vector to express a therapeutic agent for aparticular condition amenable to gene silencing therapy and theoptimization of the conditions for insertion of the selected expressionvector into the cell, are within the scope of one of ordinary skill inthe art without the need for undue experimentation.

In another embodiment, the expression vector is in the form of aplasmid, which is transferred into the target cells by one of a varietyof methods: physical (e.g., microinjection, electroporation, scrapeloading, microparticle bombardment) or by cellular uptake as a chemicalcomplex (e.g., calcium or strontium co-precipitation, complexation withlipid, complexation with ligand). Several commercial products areavailable for cationic liposome complexation including Lipofectin™(Gibco-BRL, Gaithersburg, Md.) and Transfectam™ (Promegat, Madison,Wis.). However, the efficiency of transfection by these methods ishighly dependent on the nature of the target cell and accordingly, theconditions for optimal transfection of nucleic acids into cells usingthe herein-mentioned procedures must be optimized. Such optimization iswithin the scope of one of ordinary skill in the art without the needfor undue experimentation.

VI. Diseases and Conditions Amendable to the Methods of the Invention

In the certain embodiments of the present invention, a mammalianrecipient to an expression cassette of the invention has a conditionthat is amenable to gene silencing therapy. As used herein, “genesilencing therapy” refers to administration to the recipient exogenousnucleic acid material encoding a therapeutic siRNA and subsequentexpression of the administered nucleic acid material in situ. Thus, thephrase “condition amenable to siRNA therapy” embraces conditions such asgenetic diseases (i.e., a disease condition that is attributable to oneor more gene defects), acquired pathologies (i.e., a pathologicalcondition that is not attributable to an inborn defect), cancers,neurodegenerative diseases, e.g., trinucleotide repeat disorders, andprophylactic processes (i.e., prevention of a disease or of an undesiredmedical condition). A gene “associated with a condition” is a gene thatis either the cause, or is part of the cause, of the condition to betreated. Examples of such genes include genes associated with aneurodegenerative disease (e.g., a trinucleotide-repeat disease such asa disease associated with polyglutamine repeats, Huntington's disease,and several spinocerebellar ataxias), and genes encoding ligands forchemokines involved in the migration of a cancer cells, or chemokinereceptor. Also siRNA expressed from viral vectors may be used for invivo antiviral therapy using the vector systems described.

Accordingly, as used herein, the term “therapeutic siRNA” refers to anysiRNA that has a beneficial effect on the recipient. Thus, “therapeuticsiRNA” embraces both therapeutic and prophylactic siRNA.

Differences between alleles that are amenable to targeting by siRNAinclude disease-causing mutations as well as polymorphisms that are notthemselves mutations, but may be linked to a mutation or associated witha predisposition to a disease state. An example of a targetablepolymorphism that is not itself a mutation is the polymorphism in exon58 associated with Huntington's disease.

Single nucleotide polymorphisms comprise most of the genetic diversitybetween humans. The major risk factor for developing Alzheimer's diseaseis the presence of a particular polymorphism in the apolipoprotein Egene.

Single nucleotide polymorphisms comprise most of the genetic diversitybetween humans, and that many disease genes, including the HD gene inHuntington's disease, contain numerous single nucleotide or multiplenucleotide polymorphisms that could be separately targeted in one allelevs. the other. The major risk factor for developing Alzheimer's diseaseis the presence of a particular polymorphism in the apolipoprotein Egene.

A. Gene Defects

A number of diseases caused by gene defects have been identified. Forexample, this strategy can be applied to a major class of disablingneurological disorders. For example this strategy can be applied to thepolyglutamine diseases, as is demonstrated by the reduction ofpolyglutamine aggregation in cells following application of thestrategy. The neurodegenerative disease may be a trinucleotide-repeatdisease, such as a disease associated with polyglutamine repeats,including Huntington's disease, and several spinocerebellar ataxias.Additionally, this strategy can be applied to a non-degenerativeneurological disorder, such as DYT1 dystonia.

B. Acquired Pathologies

As used herein, “acquired pathology” refers to a disease or syndromemanifested by an abnormal physiological, biochemical, cellular,structural, or molecular biological state. For example, the diseasecould be a viral disease, such as hepatitis or AIDS.

C. Cancers

The condition amenable to gene silencing therapy alternatively can be agenetic disorder or an acquired pathology that is manifested by abnormalcell proliferation, e.g., cancer. According to this embodiment, theinstant invention is useful for silencing a gene involved in neoplasticactivity. The present invention can also be used to inhibitoverexpression of one or several genes. The present invention can beused to treat neuroblastoma, medulloblastoma, or glioblastoma.

VII. Dosages, Formulations and Routes of Administration of the Agents ofthe Invention

The agents of the invention are preferably administered so as to resultin a reduction in at least one symptom associated with a disease. Theamount administered will vary depending on various factors including,but not limited to, the composition chosen, the particular disease, theweight, the physical condition, and the age of the mammal, and whetherprevention or treatment is to be achieved. Such factors can be readilydetermined by the clinician employing animal models or other testsystems, which are well known to the art.

Administration of siRNA may be accomplished through the administrationof the nucleic acid molecule encoding the siRNA. Pharmaceuticalformulations, dosages and routes of administration for nucleic acids aregenerally known.

The present invention envisions treating a disease, for example, aneurodegenerative disease, in a mammal by the administration of anagent, e.g., a nucleic acid composition, an expression vector, or aviral particle of the invention. Administration of the therapeuticagents in accordance with the present invention may be continuous orintermittent, depending, for example, upon the recipient's physiologicalcondition, whether the purpose of the administration is therapeutic orprophylactic, and other factors known to skilled practitioners. Theadministration of the agents of the invention may be essentiallycontinuous over a preselected period of time or may be in a series ofspaced doses. Both local and systemic administration is contemplated.

One or more suitable unit dosage forms having the therapeutic agent(s)of the invention, which, as discussed below, may optionally beformulated for sustained release (for example using microencapsulation,see WO 94/07529, and U.S. Pat. No. 4,962,091 the disclosures of whichare incorporated by reference herein), can be administered by a varietyof routes including parenteral, including by intravenous andintramuscular routes, as well as by direct injection into the diseasedtissue. For example, the therapeutic agent may be directly injected intothe brain. Alternatively the therapeutic agent may be introducedintrathecally for brain and spinal cord conditions. In another example,the therapeutic agent may be introduced intramuscularly for viruses thattraffic back to affected neurons from muscle, such as AAV, lentivirusand adenovirus. The formulations may, where appropriate, be convenientlypresented in discrete unit dosage forms and may be prepared by any ofthe methods well known to pharmacy. Such methods may include the step ofbringing into association the therapeutic agent with liquid carriers,solid matrices, semi-solid carriers, finely divided solid carriers orcombinations thereof, and then, if necessary, introducing or shaping theproduct into the desired delivery system.

When the therapeutic agents of the invention are prepared foradministration, they are preferably combined with a pharmaceuticallyacceptable carrier, diluent or excipient to form a pharmaceuticalformulation, or unit dosage form. The total active ingredients in suchformulations include from 0.1 to 99.9% by weight of the formulation. A“pharmaceutically acceptable” is a carrier, diluent, excipient, and/orsalt that is compatible with the other ingredients of the formulation,and not deleterious to the recipient thereof. The active ingredient foradministration may be present as a powder or as granules, as a solution,a suspension or an emulsion.

Pharmaceutical formulations containing the therapeutic agents of theinvention can be prepared by procedures known in the art using wellknown and readily available ingredients. The therapeutic agents of theinvention can also be formulated as solutions appropriate for parenteraladministration, for instance by intramuscular, subcutaneous orintravenous routes.

The pharmaceutical formulations of the therapeutic agents of theinvention can also take the form of an aqueous or anhydrous solution ordispersion, or alternatively the form of an emulsion or suspension.

Thus, the therapeutic agent may be formulated for parenteraladministration (e.g., by injection, for example, bolus injection orcontinuous infusion) and may be presented in unit dose form in ampules,pre-filled syringes, small volume infusion containers or in multi-dosecontainers with an added preservative. The active ingredients may takesuch forms as suspensions, solutions, or emulsions in oily or aqueousvehicles, and may contain formulatory agents such as suspending,stabilizing and/or dispersing agents. Alternatively, the activeingredients may be in powder form, obtained by aseptic isolation ofsterile solid or by lyophilization from solution, for constitution witha suitable vehicle, e.g., sterile, pyrogen-free water, before use.

It will be appreciated that the unit content of active ingredient oringredients contained in an individual aerosol dose of each dosage formneed not in itself constitute an effective amount for treating theparticular indication or disease since the necessary effective amountcan be reached by administration of a plurality of dosage units.Moreover, the effective amount may be achieved using less than the dosein the dosage form, either individually, or in a series ofadministrations.

The pharmaceutical formulations of the present invention may include, asoptional ingredients, pharmaceutically acceptable carriers, diluents,solubilizing or emulsifying agents, and salts of the type that arewell-known in the art. Specific non-limiting examples of the carriersand/or diluents that are useful in the pharmaceutical formulations ofthe present invention include water and physiologically acceptablebuffered saline solutions such as phosphate buffered saline solutions pH7.0-8.0. saline solutions and water.

The invention will now be illustrated by the following non-limitingExamples.

EXAMPLE 1 RNAi Silencing

The present inventors modified human mir-30 to contain sequencesspecific for genes of interest (FIG. 1). Stem base and loop sequenceswere conserved.

The inventors were able to silence a target gene with miRNA shuttles.The target gene (in this case Ataxin-1, also called SCA1) was cloned andthe SCA1 miRNA was also generated, as indicated in FIG. 2. Fluorescencemicroscopy and western blot analyses was performed and the resultsindicated dose-dependent silencing of ataxin-1 48 hours afterco-transfection of HEK293 cells with RNAi:Target plasmids.

Next, a comparison study was designed to compare silencing efficienciesof various RNAi vectors and to assess strand incorporation into RISCusing a highly sensitive, artificial reporter system. The inventorswanted to learn which vector is most optimal, and if the results wouldremain consistent independent of target. Since both siRNA strands havethe potential to enter the RISC complex, artificial RNAi targetconstructs were generated in both directions (FIG. 3). Guideantisense-strands target sense targets (e.g., SCA1-Sense), while siRNAsense-strands target anti-sense targets (e.g., SCA1-Antisense).

First, miRNA molecules were compared to “1^(st) generation” shRNAmolecules (FIG. 4). 1^(st) generation shRNAs preferentially loaded theunintended strand. Also, these shRNAs lack 2-nt 3′ overhangs that areoptimal substrates for RNAi pathway machinery.

To fairly compare RNAi strategies, optimized shRNAs (“2^(nd) generation”shRNA molecules) were designed to mimic pre-miRNAs (i.e.,Drosha-cleaved), which are indicated as arrows in FIG. 5. CorrespondingmiRNAs were generated to account for the G (U6+1) and UU (polIIIterminator) involved in shRNA transcription. Using the 2^(nd) generationshRNA molecules, RNAi against HD and SCA1 showed similar results(northern blot and siChk2 targeting) as the eGFP RNAi constructs (FIGS.6 and 7). The compilation of Dual-Glo® luciferase assay results from 10RNAi comparison experiments (4 eGFP, 4 SCA1 and 2 HD) using theartificial siChk2 targets were compared relative to mock RNAi (FIG. 8).This trend in silencing efficacy was also observed when targetingnatural eGFP and endogenous SCA1 or HD (data not shown).

Simulated Safety of RNAi Vectors

The inventors also investigated how extensively the RNAi expressionapproaches disrupt endogenous miRNA processing and function. Theinventors designed an in vitro simulated RNAi safety experiment. 293cells were transfected with U6.miGFP and siChk2-eGFP Target (1:1).Non-specific RNAi “spikes” (U6.shSCA1 or U6.miSCA1) were co-transfectedto assess their effect on miGFP-mediated silencing. In this experiment,an increase in light was evidence of toxicity (i.e., RNAi pathwaysaturation). The results indicated that in safety studies, shRNAs at lowdoses inhibit the processing of and silencing mediated by artificialmiRNAs. The results also indicated that miRNAs at high doses only causeminimal inhibition. It is important to note that the silencing efficacyof shRNA (low dose) and miRNA (high dose) are similar (FIG. 9).

The safety of RNAi in C2C12 cells was also examined (FIG. 10). TheshRNA-treated cells showed decreased cell viability as compared to themiRNA-treated cells.

In Vivo Safety of RNAi Vectors in Muscle

The inventors co-electroporated miReporter and GFP:U6.RNAi plasmids intothe tibialis anterior (shRNA:Left or miRNA:Right) (FIG. 11). IVISimaging was used for Firefly or Renilla Luciferase and GFP. Theinventors wanted to learn if there was disruption of endogenous miRNAfunction (i.e., more light) between the different vectors. The resultsshow that miRNA vectors were safe in vivo (FIG. 12).

In conclusion, the inventors found that the miRNA approach is moreeffective than 1^(st) generation shRNA; that Optimized 2^(nd) generationshRNAs silence more effectively than miRNAs; that shRNAs inhibitmiRNA-mediated silencing substantially more than the correspondingmiRNA-shuttle vectors; and that miRNA-based strategies provide safertherapeutics.

EXAMPLE 2 Silencing of HD in Mouse Striatum

AAV vectors for RNAi molecules specific for a target were injected intomouse striatum. Four months later, GFP-positive striata was harvested,and RNA was isolated. Q-PCR was performed for mouse HD and CD11b, aswell as Northern blots (FIG. 13). High-level expression from shRNAlikely explains the observed toxicity.

miRNA molecules were generated following the strategy set forth in FIGS.14 and 15.

EXAMPLE 3

An expression cassette (5′NheI-3′BglII) containing the CMV promoter,multiple cloning site (MCS) and SV40 polyadenylation signal was clonedinto TOPObluntI (XbaI-BamHI, Invitrogen™) in reverse orientation. ApolIII expression cassette containing mouse U6 promoter, MCS andPolIII-terminator (6T's) was cloned into TOPObluntII with the samestrategy. miRNA shuttles were generated by polymerase extension ofoverlapping DNA oligonucleotides (IDT). Polymerase-extended productswere digested with XhoI-SpeI and cloned in the MCS of the expressionvectors XhoI-SpeI (miV1) or XhoI-XbaI (miV2). shHD2.1 production hasbeen previously described. Other shRNAs were cloned using a tailed-PCTstrategy. PCR products containing U2-shRNA-6T's were TOPO cloned intothe bluntII vector and positive clones were considered to be in reverseorientation to maintain consistency with the other expression vectors.

RNAi luciferase reporter vectors were constructed using psiCheck2(Promega®). Tailed-PR was used to amplify a 3′ fragment of Renillaluciferase containing a single, perfect complementary RNAi Target site(˜25 bp: 21 bp target+2 nt 5′ and 3′) downstream of the stop codon. ThisPCR product was digested with AatII-XhoI and cloned into the same siteswithin psiCheck2. The vector sequences are shown in FIG. 16. FIG. 19shows additional miRNA sequences that were used to target either HD orSCA1. These are the predicted RNA stem loop structures that contain theactive RNAi sequences. The active antisense strand of the embedded siRNAsequence is underlined.

FIG. 17 shows the basic miRNA structure of Variant 2. Variant 1 andVariant 3 form unique structures which direct less efficient Droshaprocessing than Variant 2. It was unexpected that Variant 2 would bemuch more efficient than Variants 1 and 3, based on the designalgorithm.

Variants 1 and 3 may provide alternatives to further de-dose RNAistrategies. If one desired a high degree of knock-down, then one woulduse Variant 2. If, however, a lesser degree of knock-down was desired,one would use Variant 1 or 3. The boxed region shown in FIG. 17indicates a region that affects silencing efficiency, presumably byinfluencing Drosha cleavage efficiency or accuracy. The region islocated in the stem-base 10-12 base pairs away from the Drosha cleavagesites. Silencing efficiency was improved when this region was madeunstable (i.e., no base pairing or bulged loop). Silencing efficiency isreduced when this region is made more stable (i.e., base pairing, no orsmall loop). Variants 1 and 3 contain more stable conformations and,hence, are less efficient than Variant 2.

To improve the RNAi strategy, the inventors investigated the use ofartificial miRNAs as siRNA shuttles. The inventors modified the humanmiR-30 primary transcript by replacing the mature miR-30 region (˜20-bpduplex which is excised via sequential Drosha and Dicer processing) withdesired siRNA sequences (FIG. 18A). The structure of miR-30 has beenwell-characterized, and the major Drosha and Dicer cleavage sites havebeen experimentally validated. The inventors generated artificial miRNAscontaining the structural elements within the stem-base required foreffective Drosha processing but otherwise devoid of natural miR-30flanking sequences. With this strategy, the flanking sequences (˜35-ntupstream and ˜40-nt downstream) arise from the vector sequence withinthe multiple cloning site (MCS). Although the minimal sequence elementsnecessary for miR-30 processing are known, the effects of flankingsequences, and consequently the transcript structure within the nearbystem-loop base, on processing efficiency has not been evaluated. To testthis, the inventors generated miR-30 shuttle variants predicted to formunique RNA structures proximal to the base of an identical miRNAstem-loop (FIG. 18A,B). Luciferase reporters containing a siRNA targetsite (˜25-bp) within the 3′UTR, herein referred to as RNAi luciferasereporters (FIG. 18C), were developed to assess silencing efficiencies inco-transfection studies. The variant flanking sequences influencedsilencing efficacy relative to the same miRNA stem-loop flanked bynatural human miR-30 sequences (FIG. 18D). Notably, one miRNA variant(miV2) yielded 20% more gene knockdown than the natural miR-30 structure(P<0.01). This improved silencing was likely the result of improvedprocessing, as miV2 generated the most antisense RNA as determined bysmall transcript northern blot. Interestingly, miV2 exhibits a region ofsingle-stranded nature (FIG. 18B, shaded region) that may promotebinding of the Drosha-DGCR8 complex, as supported by models forpri-miRNA processing.

EXAMPLE 4 Minimizing Variables Among Hairpin-Based RNAi Vectors Revealsthe Potency of shRNAs

RNA interference (RNAi) is an evolutionarily conserved cellular processregulating gene expression and participating in innate defense againsttransposable elements and viral invasion. RNAi mediatessequence-specific gene silencing by double-stranded RNAs (dsRNAs) whichmay be processed by Dicer into functional small RNAs [small interferingRNAs (siRNAs) and microRNAs (miRNAs) among others]. Small RNAsassociated with the RNA-induced silencing complex (RISC) or RISC-likecomplexes mediate post-transcriptional gene silencing by targetingtranscripts for degradation or translational repression. Also, smallRNAs in RISC-like complexes may direct heterochromatin formation tomediate transcriptional gene silencing.

RNAi has been utilized as a tool to query gene function and is beingdeveloped as a modality for disease therapy. Exogenous RNAi has beenexpressed in cultured cells and organisms as short-hairpin RNAs (shRNAs)or artificial miRNAs (FIG. 18A). The basic transcriptional unit of ashRNA is sense and antisense sequences connected by a loop of unpairednucleotides. shRNAs are exported from the nucleus by Exportin-5, andonce in the cytoplasm, are processed by Dicer to generate functionalsiRNAs. miRNA stem-loops are typically expressed as part of largerprimary transcripts (pri-miRNAs). The Drosha-DGCR8 complex excises thestem-loops generating intermediates known as pre-miRNAs, which aresubsequently exported to the cytoplasm and diced into functional smallRNAs.

Previous studies from several laboratories, including that of theinventors, demonstrate the utility and efficacy of shRNAs in vitro andin vivo. However, the use of artificial miRNAs (pri-miRNA scaffoldsshuttling siRNA sequences) as RNAi vectors has become an attractivealternative. Artificial miRNAs more naturally resemble endogenous RNAisubstrates and are more amenable to Pol-II transcription (allowingtissue-specific expression of RNAi) and polycistronic strategies(allowing delivery of multiple siRNA sequences). A persistent questionin the field, however, is which RNAi expression system is most optimalfor achieving gene silencing in particular applications.

Optimization of RNAi strategies remains important due to the potentialside-effects caused by exogenously delivered RNAi. RNAi vectors maycompete for endogenous RNAi machinery, stimulate cellular responses todsRNA, or silence unintended target mRNAs due to partialcomplementarity. These side effects can produce severe cellular toxicityand even result in organismal death. Improved RNAi-based gene silencingstrategies may allow delivery of lower doses, thus reducing thelikelihood of RNAi-related side-effects.

To date, shRNA- and artificial miRNA-based strategies have been comparedwith conflicting results. In certain comparisons, the shRNAs tested hadsub-optimal 5′ overhangs due to variable arrangements of transcriptionstart and stop sequences, some caused inadvertently by the use ofrestriction enzyme sites during vector production. This raises concernssince recent reports have demonstrated that 2-nt 3′ overhangs, oftenobserved in natural pre-miRNAs, are optimal substrates for Exportin-5and Dicer. Furthermore, none of the prior hairpin-based comparisonsassessed the equivalency of strand-biasing. Strand-biasing refers towhich strand of the siRNA duplex enters the RISC and mediates genesilencing. In general, the strand with the weakest base-pairing near the5′ end will be incorporated into the RISC. Hence, shRNA and artificialmiRNA comparisons may be confounded if the vectors, followingprocessing, release siRNAs which exhibit differential strand-biasing(i.e., one loading the intended antisense strand and the other loadingthe unintended sense strand). Indeed, a single base-pair shift duringRNAi substrate processing may alter which strand of the resulting siRNApreferentially enters the RISC, thus highlighting the importance ofevaluating strand-biasing in RNAi vector comparison studies.

The present inventors have demonstrated how early-generation shRNAs withpoor strand-biasing confound the comparison of hairpin-based RNAiapproaches. Minimizing the variables for comparison reveals that, forthree independent target sequences and in different settings (in vitroand in vivo), shRNAs are more potent than artificial miRNAs.

Results

Development of an Improved miR-30-Based siRNA Shuttle

The inventors have previously demonstrated the therapeutic efficacy ofshRNAs in mouse models of neurodegenerative diseases [SpinocerebellarAtaxia Type I (SCA1) and Huntington's disease (HD)] (Xia et al., NatMed, 10(8), 816-820 (2004); Harper et al., 2005, PNAS, 102: 5820-5825).To improve the RNAi strategy, the inventors investigated the use ofartificial miRNAs as siRNA shuttles. The inventors modified the humanmiR-30 primary transcript by replacing the mature miR-30 region (˜20-bpduplex which is excised via sequential Drosha and Dicer processing) withdesired siRNA sequences (FIG. 18A). The structure of miR-30 has beenwell-characterized, and the major Drosha and Dicer cleavage sites havebeen experimentally validated. The inventors generated artificial miRNAscontaining the structural elements within the stem-base required foreffective Drosha processing but otherwise devoid of natural miR-30flanking sequences. With this strategy, the flanking sequences (˜35-ntupstream and ˜40-nt downstream) arise from the vector sequence withinthe multiple cloning site (MCS). Although the minimal sequence elementsnecessary for miR-30 processing are known, the effects of flankingsequences, and consequently the transcript structure within the nearbystem-loop base, on processing efficiency has not been evaluated. To testthis, the inventors generated miR-30 shuttle variants predicted to formunique RNA structures proximal to the base of an identical miRNAstem-loop (FIG. 18A,B). Luciferase reporters containing a siRNA targetsite (˜25-bp) within the 3′UTR, herein referred to as RNAi luciferasereporters (FIG. 18C), were developed to assess silencing efficiencies inco-transfection studies. The variant flanking sequences influencedsilencing efficacy relative to the same miRNA stem-loop flanked bynatural human miR-30 sequences (FIG. 18D). Notably, one miRNA variant(miV2) yielded 20% more gene knockdown than the natural miR-30 structure(P<0.01). This improved silencing was likely the result of improvedprocessing, as miV2 generated the most antisense RNA as determined bysmall transcript northern blot (FIG. 18E). Interestingly, miV2 exhibitsa region of single-stranded nature (FIG. 18B, shaded region) that maypromote binding of the Drosha-DGCR8 complex, as supported by models forpri-miRNA processing.

Strand-Biasing Confounds Hairpin-Based Comparisons

The inventors next developed miR-30 shuttles (miV1 and miV2) containingsiRNA sequences based on HD2.1 [targets the transcript of the humanHuntington's disease (HD) gene] to compare to the short-hairpin shHD2.1(a shRNA previously tested in therapeutic efficacy studies in a mousemodel for HD (Harper et al., 2005, PNAS, USA 102: 5820-5825)). Theprocessing of CMV-driven miHD2.1 variants and U6-driven shHD2.1 wasassessed by small transcript northern blot analysis (FIG. 4A). ThemiRNA-based shuttles yielded more antisense RNA than the shRNA vectorwhich generated an abundance of unprocessed precursor stem-loop RNAs.Also, miV2 generated more antisense RNA than miV1 as previously observedin FIG. 18E. Importantly, the improvement of the artificial miRNAs overthe shRNA was not the result of promoter discrepancies since theU6-miRNA vectors were even more potent than the CMV-miRNA vectors (FIG.26; P<0.01).

The silencing efficiencies of CMV-miHD2.1(V2) and U6-shHD2.1 againstendogenous HD transcripts were assessed by Q-PCR following transfectionof RNAi expression vectors into human-derived HEK293 cells. Consistentwith our northern blot results, miHD2.1 demonstrated approximately 50%improved silencing of endogenous HD mRNA relative to shHD2.1 (FIG. 4B;P<0.05). These findings support prior data showing that miRNA-basedstrategies are more potent than first-generation shRNAs. However,because recent work has shown that strand-biasing affects siRNA-mediatedgene silencing, the inventors tested whether shHD2.1 and miHD2.1 (bothU6-driven) preferentially load the intended antisense strand orunintended sense strand. The inventors designed RNAi luciferasereporters containing either sense or antisense target sites to evaluatethe silencing activity of each strand. Co-transfection studies revealedthat shHD2.1 preferentially silenced the unintended target, whilemiHD2.1 favored silencing of the intended strand (FIG. 4C). These dataare important as they demonstrate that disparate strand-biasing canconfound comparisons of shRNA- and miRNA-based approaches.

shRNA Expression and Potency is Overhang-Dependent

To more fairly compare shRNA- and miRNA-based silencing strategies, theinventors designed shRNAs using the predicted structure ofDrosha-cleaved miR-30 stem-loops as a design guide. These shRNAs weredesigned to have minimized 3′ overhangs (2-4 Us resulting from Pol-IIItermination) to resemble the 2-nt 3′ overhangs which result from Droshacleavage. Overhangs of this length provide optimal substrates forExportin-5 and Dicer. In addition, target sequences were selected toaccount for the +1-G nucleotide of the mouse U6 promoter and to containAU-rich 3′ ends, both of which promote loading of the antisense strand.While designing shRNAs in this manner is becoming common practice, theinitial shRNA-miRNA comparison studies tested shRNAs with sub-optimaloverhangs. Hence, the inventors revisited testing the effects of shRNAoverhangs (5′ and 3′) on processing and silencing efficiency. Theinventors developed a series of vectors expressing a common shRNA butwith altered overhang lengths, in certain cases, resembling those (i.e.,5′ variants) found in previous shRNA and artificial miRNA comparisonstudies (FIG. 21A). Northern blot and densitometry analyses showed thatshRNAs with the minimal 3′-U₂₋₄ overhangs yield 3- and 4-fold morepre-shRNA (unprocessed) and antisense RNA (processed), respectively,than shRNAs with 5′-overhangs (FIG. 21B). Unexpectedly, shRNA expressionlevels appear to decrease with lengthening 5′ or 3′ overhangs. Theinventors presume that sub-optimal overhangs lower shRNA transcriptstability, considering that all variants were expressed by the samemouse U6 promoter and only differ by up to 27-nt in length.

In gene silencing studies targeting a co-transfected RNAi luciferasereporter, the inventors found that shRNAs with minimal overhangs(3′-U₂₋₄ or 3′-CU₂₋₄) overhangs were most effective (P<0.001), whileefficiency is compromised upon increasing 5′ or 3′ overhangs (FIG. 21C).Northern blot analyses and gene silencing studies targeting sense orantisense RNAi luciferase reporters demonstrated that each shRNA variantfavored loading of the intended antisense strand (FIG. 21B,C). WhileshRNAs with longer overhangs demonstrate slightly reducedintended:unintended silencing ratios, their decreased silencingefficiencies likely result from reduced transcript stability andprocessing as supported by our northern blot data.

Minimizing the Variables Between Artificial miRNA and shRNA Vectors forComparison

Next, the inventors sought to compare the improved artificial miRNAs(FIG. 18, miV2) and shRNAs (FIG. 22A, 3′U₂₋₄) for processing andsilencing efficiency. To test for consistency of results independent oftarget and sequence, the inventors designed shRNA- and miRNA-basedvectors targeting SCA1, HD, and GFP mRNAs—the former two providingconstructs to further test in therapeutic development. Importantly, andunique from other shRNA and miRNA comparisons (Boden et al., 2004,Nucleic Acids Res 32: 1154-1158; Silva et al., 2005, Nat Genet. 37:1281-1288; Li et al., 2007, RNA 13: 1765-1774), the inventors'artificial miRNAs were adjusted to account for nucleotide restrictionsassociated with Pol-III transcription of shRNAs (FIG. 22A,B). Hence,following Drosha-cleavage, the pre-miRNAs would be comparable to theshRNAs and subsequent processing of each stem-loop by Dicer would yieldsimilar siRNA species. This is an important consideration since a singlebase-pair shift may alter the strand-biasing or potency of the resultingsiRNA.

To evaluate the processing of the current vectors, the inventorsperformed 3′-RACE to identify the 3′ ends of the sense and antisensestrands of siRNAs generated by corresponding artificial miRNA and shRNAexpression vectors (FIG. 27). To date, none of the RNAi vectorcomparison studies have performed this important analysis to test theequivalency of processing between the compared vectors. The inventors'3′-RACE analyses revealed that both RNAi vectors generate at least foursiRNA species which were common between the vectors. These findings areconsistent with a previous report which demonstrated flexibility (i.e.base-pair shifting) in dsRNA cleavage by Dicer (Vermeulen et al., 2005,RNA 11: 674-682). Notably, the most prevalent species generated by theRNAi vectors was shared, representing approximately 50% of the 3′-RACEsequences analyzed (n=10-12 per vector per strand). These resultssupport the integrity of comparing artificial miRNAs and shRNAs designedwith the present strategy.

Next, the inventors assessed the strand-biasing of these RNAi vectors bytargeting sense or antisense RNAi luciferase reporters, sinceinconsistent strand-biasing confounded our original comparison (FIG. 4).In all three RNAi vector-pairs (SCA1, HD, and GFP), a strong preferencefor silencing the intended strand was observed for both artificialmiRNAs and shRNAs (FIG. 23). For the SCA1 and GFP vectors, neither ofthe RNAi expression strategies silenced the unintended targets, and onlyminimal activity of the unintended strand was observed with the HD RNAivectors. These results demonstrate that the desired strand-biasing isconsistent for each RNAi vector-pair, thus maintaining their suitabilityfor further comparison studies.

shRNAs Show Improved Potency Relative to Artificial miRNAs

As an initial comparison of gene silencing efficacy, the RNAi vectorsand their respective RNAi luciferase reporters were co-transfected intoHEK293 cells. Luciferase assay data from several experiments (n=4 SCA1,n=2 HD and n=4 GFP) were compiled, revealing that optimized shRNAs aremore potent than artificial miRNAs independent of the RNAi doses testedand target sequence [FIG. 24A; P<0.001 and P<0.05 for 1:1 and 3:1(RNAi:Target) doses respectively]. Notably, this improved efficacy ofthe shRNAs was also observed per vector-pair in our previousstrand-biasing studies (FIG. 23).

Though targeting RNAi luciferase reporters provides a quantitative andfacile means for assessing gene silencing, the inventors also wanted toevaluate the capacities for these RNAi vectors to silence their naturaltargets. In HEK293 cells transfected with RNAi expression plasmids,silencing trends of shRNA>miRNA were also observed when targetingendogenous SCA1 or HD transcripts (FIG. 24B,C; P<0.05 and P<0.001respectively). Furthermore, the shRNA targeting GFP demonstratedimproved potency over the corresponding artificial miRNA followingco-transfection of RNAi and GFP expression plasmids into HEK293 cells(FIG. 24D; P<0.01).

Next, the inventors compared the processing efficiencies of ourartificial miRNA and shRNA vector-pairs in vitro following transfectionof RNAi expression plasmids. Small transcript northern blots demonstratethat, unlike the first-generation shRNAs (FIG. 4A), the optimized shRNAsproduce at least 4-fold more antisense RNA as compared to artificialmiRNAs independent of target (FIG. 24E). This improved yield likelyresults from higher expression levels since optimized shRNAs stillgenerate high levels of precursor, whereas artificial miRNAs showminimal build-up of pri- or pre-transcripts.

In vivo applications of RNAi are becoming widely used to study genefunction or develop therapeutics. As such, the inventors compared one ofthe present vector-pairs (shSCA1 and miSCA1) for gene silencing in mice.Since these constructs target human SCA1, and not mouse SCA1, theinventors measured in vivo silencing of a co-delivered SCA1 RNAiluciferase reporter. RNAi and RNAi luciferase reporter plasmids wereco-electroporated into the tibialis anterior muscles of mice, andbioluminescence imaging was performed to determine in vivo genesilencing at 4 and 8 days post-treatment. At 1:1 and 10:1 (RNAi:Target)ratios, shRNAs show improved potency over artificial miRNAs (FIG. 25).These results, together with the in vitro data, demonstrate that shRNAscan be more potent than miRNAs independent of target and experimentalsetting (in vitro and in vivo).

Discussion

The inventors have developed a novel miR-30-based siRNA shuttle whichshows improved potency over the commonly used miR-30 shuttle whichcontains natural miR-30 flanking sequences. miRNA-based approachesprovide an attractive alternative to classic shRNAs; hence, theinventors compared the efficiencies of these systems in mediating genesilencing.

The inventors present data demonstrating that shRNA and artificial miRNAcomparison analyses must be carefully controlled, as differentialstrand-biasing between the compared vectors may generate misleadingresults. This possibility, in addition to the use of shRNAs withsub-optimal overhangs, may explain the discrepancies among previouslypublished hairpin-based comparisons studies. The present analysesprovide a fair comparison of shRNA- and miRNA-based vectors, taking intoconsideration the transcribed product, processing sites, andstrand-biasing. When variables between the two systems are minimized,shRNAs demonstrate improved silencing efficacy relative to theirmiRNA-based counterparts. The present experiments are unique in that theinventors carefully controlled vector design (e.g., maintainedstem-length and loop structures between compared vectors), assessed theequivalency of siRNAs generated and strand-biasing, and validated theimproved potency of shRNAs in vivo. Furthermore, the inventorsdemonstrate that shRNAs yield abundant levels of precursor and fullyprocessed antisense RNA relative to artificial miRNAs, thus providingmechanistic insight to explain the increased potency.

General users of RNAi must carefully consider the balance of efficacyand toxicity when selecting the most suitable RNAi expression strategy.The improved potency of optimized shRNAs may be offset by toxicityissues; high levels of RNAi substrates (processed and unprocessed)generated from shRNA expression vectors may saturate cellular RNAimachinery, thus interfering with endogenous miRNA biogenesis andfunction in cell culture and in vivo.

The robust expression of optimized shRNAs may be desirable for certainapplications. For example, toxicity is likely minimized in low-copyapplications such as the generation of stable cell lines via retroviralvectors, which typically transduce at few to one copy per cell. Hence,shRNAs may be better suited than miRNA-based vectors where low-levelexpression would preclude sufficient silencing. Alternatively, shRNAsmay be advantageous when silencing highly expressed targets which mayoutcompete low levels of antisense RNA; for example, therapeutictargeting of invasive viruses or cancers, where limiting toxicity maynot be the highest priority.

For some applications, high vector doses must be delivered to achieveefficient transduction of a cell population. Hence, shRNA strategies maybe undesirable if vector copies per cell cannot be readily limited, asoften occurs in vivo, and minimizing toxicity is of high priority. Inaddition to saturation-based toxicity, high levels of siRNAs may promotesilencing of unintended targets via partial complementarity. Hence,utilizing artificial miRNAs, which exhibit lower expression, may providea unique opportunity to limit RNAi substrate levels when large vectordoses must be administered to achieve efficient cell-targetingthroughout a given tissue. This concept is particularly relevant to thedevelopment of therapeutic RNAi, where transduction efficiency andvector safety are of the utmost importance.

Inevitably, the selection of which hairpin-based RNAi expression systemis most suitable for a given application relies on several factors:project goals, delivery options, target expression levels, and desiredsilencing efficiency. The approach outlined here, where variables ofstrand-biasing and processing are minimized, can help guide researchersin identifying suitable vectors for their RNAi-based applications.

Material and Methods

Vector Design

An expression cassette (5′NheI-3′BglII) containing the CMV promoter,multiple cloning site (MCS) and SV40 polyadenylation (polyA) signal wascloned into TOPO-BluntII (XbaI-BamHI, Invitrogen™) in reverseorientation. A Pol-III expression cassette containing mouse U6 promoter,MCS and Pol-III-terminator (6T's) was cloned into TOPO-BluntII with thesame strategy. Artificial miRNAs were generated by polymerase extensionof overlapping DNA oligonucleotides (IDT). Polymerase-extended productswere digested with XhoI-SpeI and cloned into the MCS of the expressionvectors XhoI-SpeI (miV1) or XhoI-XbaI (miV2). miV3 resulted from anunexplained cloning error. shHD2.1 has been previously described (Harperet al., 2005, PNAS, USA 102: 5820-5825). Other shRNAs were cloned usinga tailed-PCR strategy. PCR products containing U6-shRNA-6T's were TOPOcloned into the BluntII vector and positive clones were considered to bein reverse orientation to maintain consistency with the other expressionvectors.

For in vivo studies, miRNA or shRNA expression cassettes driven by themouse U6 promoter were cloned in the same orientation upstream of aCMV-hrGFP-SV40polyA expression cassette.

RNAi luciferase reporter vectors were constructed using psiCheck2(Promega®). Tailed-PCR was used to amplify a 3′ fragment of Renillaluciferase containing a single, perfect complementary RNAi target site(˜25-bp: 21-bp target+2-nt 5′ and 3′) downstream of the stop codon. ThisPCR product was digested with AatII-XhoI and cloned into the same siteswithin psiCheck2.

See FIG. 16 and FIG. 28 for detailed information about vectorconstruction.

3′-RACE Analyses

HEK293 cells grown in 6-well plates were transfected (Lipofectamine™2000, Invitrogen™) with RNAi expression plasmids (200 ng or 2 μg forshRNA and artificial miRNA plasmids respectively). Total RNA wasisolated at 48 h post-transfection using 1 ml TRIzol® reagent(Invitrogen™). Subsequently, 250 ng of total RNA was treated withA-Plus™ Poly(A) polymerase (Epicentre®), and then subjected tofirst-strand cDNA synthesis using an anchored oligo-dT primer containinglinker sequence (RLM-RACE, Ambion®; TaqMan® reverse transcriptionreagents, Applied Biosystems). PCR was performed using the followingprimers: 5′-TTAATACGACTCACTATAGGT-3′ (SEQ ID NO: 210) (linker primer),5′-ACTTCAACGCTGACCT-3′ (SEQ ID NO: 211) (SCA1 antisense RACE) and5′-CCAGGTCAGCGTTGA-3′ (SEQ ID NO: 212) (SCA1 sense RACE). Products wereTOPO cloned into the pCR2.1 vector (Invitrogen™) and sequenced.

Northern Blot Analyses

HEK293 cells grown in 6-well plates were transfected with 1.5 μg of RNAiexpression plasmid. Total RNA was isolated at 48 h post-transfectionusing 1 ml TRIzol® reagent (Invitrogen™); alternatively, the small RNAfraction was harvested using mirVana Isolation Kit (Ambion®). 15-20 μgtotal RNA or 1-2 μg small RNA fraction was resolved on a 15% acrylamidegel. Small transcript sizes were determined with the Decade Ladder(Ambion®). Consistent loading and RNA integrity was assessed by ethidiumbromide stain. RNA was transferred to Hybond™-XL membrane (AmershamPharmacia) at 200-400 mA for 1-2 h and UV-crosslinked with theauto-crosslink function on a Stratalinker® 1800 (Stratagene®). Blotswere pre-hybridized using UltraHyb-Oligo (Ambion®) at 35° C., probedwith ³²P-labeled oligonucleotides (Ready-To-Go T4 polynucleotide kinase;Amersham) at 30-35° C. overnight, washed three times (5 min each) in2×SSC, 0.1% SDS at 30-35° C., and exposed to film. Alternatively, blotswere probed with biotin-labeled oligonucleotides and analyzed using theBio-Detect Kit (Ambion®). Densitometry analyses were performed using abioimaging system (UVP) coupled with LabWorks software (UVP).

Quantitative Real-Time PCR Analyses

HEK293 cells grown in 24-well plates were transfected with 700 ngRNAi-expressing plasmids. At 48 h post-transfection, total RNA wasisolated with 0.5 ml TRIzol® reagent (Invitrogen™), and random-primedfirst-strand cDNA synthesis was performed using 1 μg total RNA (TaqMan®reverse transcription reagents; Applied Biosystems) per manufacturer'sprotocol. Assays were performed on a sequence detection system usingprimers-probe sets specific for human HD, SCA1, GAPDH or 18S rRNA (Prism7900HT and TaqMan® 2× Universal Master Mix; Applied Biosystems).Relative gene expression was determined by using the relative standardcurve method.

GFP Silencing Analyses

HEK293 cells grown in 12-well plates were transfected with 1.2 μg and300 ng of RNAi (SCA1 or GFP) and eGFP expression plasmids respectively.At 48 h post-transfection, fluorescent photomicrographs were captured at4× magnification using an Olympus IX70 (microscope) and DP70 (camera)coupled with Olympus DP Controller software. Mean fluorescence in eachimage was determined using the histogram function in Image J software(NIH). Results for GFP RNAi-treated cells were normalized to controlSCA1 RNAi-treated cells.

In Vitro Luciferase Assays

HEK293 cells grown in black 96-well plates (Costar 3603; Corning Inc.)were co-transfected in triplicate with RNAi-expressing plasmids (1-60ng) and RNAi luciferase target plasmids (10-20 ng). In dosing studies,empty-vector was supplemented to low doses to match total DNA load.Firefly and Renilla luciferase activities were assessed 24 hpost-transfection using the Dual-Glo Luciferase Assay System (Promega®)per manufacturer's instructions, using 50 μl per substrate. Luminescentreadings were acquired with a 96-well plate luminometer (Dynex). Resultswere calculated as the quotient of Renilla/Firefly luciferaseactivities.

In Vivo Luciferase Assays

Animal studies were approved by the University of Iowa Animal Care andUse Committee. Eight-week old male C57/BL6 mice (Jackson Laboratories)were anesthetized with ketamine-xylazine and injected with 30 μl of 0.4U/μl hyaluronidase (Sigma) into the tibialis anterior (TA) muscle. Twohours later, plasmids in 30 μl saline were injected into the TA muscleof re-anesthetized mice were. All groups (n=4 muscles) received 1 μgRNAi luciferase reporter plasmid along with 10 μg empty vector or RNAiplasmid (high dose) or 9 μg empty vector and 1 μg RNAi plasmid (lowdose). Plasmids were prepared using the EndoFree® Plasmid Maxi Kit(Qiagen®). Plasmid-injected muscles were electroporated as previouslydescribed (McMahon et al., 2001, Gene Ther 8: 1264-1270) applying 175V/cm in 10 20 ms pulses at 2 Hz (ECM 830 electroporator, BTX). At 4 and8 days post-treatment, mice were sedated with isoflurane, and 30 μl ofcoelenterazine (0.3 mg/ml, Promega®) was injected into the TA muscles.Bioluminescence imaging was performed immediately using an IVIS200imaging system (Xenogen). Light emissions were analyzed using LivingImage software (Xenogen) and Igor Pro image analysis software(WaveMetrics Inc.). Data collected at 4 and 8 d revealed similarsilencing trends (4 days not shown).

Statistical Analyses

Student's t-Test was used for all studies where P-values are provided.In all statistical analyses, P<0.05 was considered significant.

EXAMPLE 5 Artificial microRNAs Demonstrate Improved Safety OverShort-Hairpin RNAs

RNA interference (RNAi) is an evolutionarily conserved cellular processregulating gene expression and participating in innate defense. RNAidirects sequence-specific gene silencing by double-stranded RNAs(dsRNAs) that may be processed by Dicer into functional small RNAs, suchas small interfering RNAs (siRNAs) and microRNAs (miRNAs) among others.Small RNAs associated with the RNA-induced silencing complex (RISC) orRISC-like complexes mediate post-transcriptional gene silencing bytargeting transcripts for degradation or translational repression.

RNAi has been utilized as a biological tool to study gene function andis being developed as a therapeutic strategy to treat several diseases.Exogenous RNAi has been expressed in cell cultures and animals asshort-hairpin RNAs (shRNAs) or artificial miRNAs, such as primary miRNA(pri-miRNAs) transcripts serving as siRNA shuttles. shRNAs areclassically transcribed as sense and antisense sequences connected by aloop of unpaired nucleotides. Following transcription, shRNAs areexported from the nucleus by Exportin-5, and processed by Dicer in thecytoplasm to generate functional siRNAs. miRNA stem-loops are typicallyexpressed as part of larger pri-miRNA transcripts. These stem-loops areexcised by the Drosha-DGCR8 generating intermediates known aspre-miRNAs, which are subsequently exported to the cytoplasm and dicedinto functional small RNAs.

While several studies from independent laboratories have demonstratedtherapeutic efficacy of shRNAs in mouse models for neurological disease,few studies have rigorously evaluated the safety of RNAi vectors. Todate, most expression-based RNAi strategies have utilized shRNAsexpressed at high levels from strong Pol-III promoters. High levels ofexogenously supplied RNAi substrates may cause cellular toxicity byvarious means. RNAi substrates may compete for endogenous RNAimachinery, thus disrupting natural miRNA biogenesis and function.Alternatively, shRNA expression can stimulate cellular responses todsRNA, which may result in global gene silencing. Finally, toxicity mayresult from an increased likelihood of off-target silencing ofunintended mRNAs due to partial complementarity with the seed region(positions 2-8, important for translational repression-based silencing)of antisense RNAs. These side-effects can produce severe cellulartoxicity and even result in organismal death.

The inventors tested corresponding shRNA- and miRNA-based expressionvectors which, upon processing, yield similar siRNA sequences withcomparable strand-biasing. The inventors evaluated the safety of thesevectors in vitro and in vivo and present data further supporting thatartificial miRNAs show improved safety profiles over shRNAs. Inaddition, the inventors demonstrate that artificial miRNAs are effectivein silencing a therapeutic target in a mouse model for neurodegenerativedisease.

Results

Effects of Hairpin-Based RNAi Vectors on miRNA Biogenesis and Function

The inventors previously compared the efficacy of shRNAs and artificialmiRNAs using a fair comparison scheme by minimizing the variablesbetween the vectors (FIG. 29). They found shRNAs to be more potent;however, they noted that shRNAs are expressed at very high levels andyield an abundance of unprocessed precursors, whereas, artificial miRNAsare expressed at lower levels and processed efficiently. The inventorshypothesized that shRNAs saturate cellular RNAi processing machinery,and thus, are more prone to interfere with miRNA biogenesis andfunction.

Initially, the relative safety of U6-driven shRNA- and miRNA-based RNAivectors in vitro were tested by competition assay. The effects of theseRNAi strategies on the processing and function of exogenously suppliedartificial miRNAs were tested. This approach was used to simulate theprocessing of endogenous miRNAs while avoiding the possibility of havingpre-processed mature miRNAs, which may be quite stable, present prior tothe initiation of the experiment. In these studies, plasmids expressingmiGFP and a GFP RNAi luciferase reporter, which contains a perfecttarget site for the GFP RNAi sequence, were co-transfected into HEK293cells to establish baseline silencing mediated by a miRNA-based vector.Next, alleviation of silencing upon the co-expression of shSCA1 ormiSCA1 competitors was evaluated to measure the potential interferenceimparted on miGFP activity. The inventors found that shSCA1significantly decreases the function of miGFP (FIG. 30A). Notably,miSCA1, at a 10-fold higher dose, only slightly hindered miGFP activity.Interestingly, at this high dose, miSCA1 demonstrated similar silencingefficacy as the low dose of shSCA1 when targeting the SCA1 RNAiluciferase reporter in parallel experiments (FIG. 30B). These resultswere supported by reciprocal experiments where the effect of GFP RNAicompetitors (shGFP or miGFP) on miSCA1 activity was evaluated inparallel with GFP RNAi efficacy studies (FIG. 30C,D).

To evaluate whether shRNA expression disrupts miRNA biogenesis (e.g., bysaturating Exportin-5 or Dicer) or function (e.g., by saturating RISC),the inventors performed northern blot analysis to assess the processingof miGFP in the presence of shSCA1 or miSCA1 competitors. They foundthat miGFP was appropriately processed to the mature form whenco-expressed with miSCA1 competitors (FIG. 30E, top panel). Conversely,miGFP biogenesis was severely disrupted in the presence of shSCA1expression vectors at low and high doses. This interference likelyresulted from the robust shSCA1 expression which generated abundantprecursor and processed forms relative to miSCA1 (FIG. 30E, bottompanels). These data, together with the inventors' gene silencing studies(FIG. 30B), suggest that maximal silencing can be achieved withmiRNA-based approaches without build-up of undesired precursor andprocessed products which disrupt miRNA biogenesis and function.

The inventors subsequently tested the effects of the shRNA- andmiRNA-based RNAi strategies on endogenous miRNA biogenesis and functionusing mouse muscle-derived C2C12 cells, which upon differentiationinduce expression of miR-1, a muscle-specific miRNA. This induction wasevaluated by measuring the activity of a luciferase reporter for miR-1function in undifferentiated and differentiated C2C12 cells (FIG.31A,B). Next, it was tested whether shSCA1 or miSCA1 expression disruptsthe induction of miR-1 activity during differentiation. Consistent withour previous data, shSCA1 almost entirely inhibited miR-1 activationwhile miSCA1 expression had negligible effects (FIG. 31B).

Inhibiting the function of muscle-specific miRNAs in differentiatingC2C12 cells has been shown to disrupt the elongation process duringmyotubes formation. The inventors, therefore, measured the elongation ofdifferentiated C2C12 cells following transfection with shRNA orartificial miRNA expression plasmids that co-express CMV-driven hrGFP(FIG. 31C). At 72 h post-treatment and differentiation,immunocytochemistry was performed to label myosin heavy-chain (MHC) toidentify differentiating myotubes, and the relative lengths of MHC+/GFP+cells were measured (FIG. 31D). The inventors found that the elongationprocess was significantly reduced in C2C12 cells transfected withshSCA1-expressing plasmids, but not those expressing miSCA1 (FIG. 31E,P<0.01).

Effects of Hairpin-Based RNAi Vectors on Cell Viability

During the C2C12 studies, the inventors observed less overallhrGFP-positivity in shSCA1-treated cells at 72 h post-transfection. Theinventors hypothesized that this loss was the result of shRNA-inducedtoxicity. Thus, the survival of RNAi-transfected C2C12 cells wasassessed by monitoring the co-expression of hrGFP by fluorescencemicroscopy over a time-course (FIG. 32). At 24 h post-transfection, eachtreatment (No RNAi, miSCA1, or shSCA1) showed similar levels offluorescence. However, at 72 h, the inventors noted a clear loss ofhrGFP-positive cells in the shSCA1-treated population and no effect ineither of the other treatment groups. At 72 hours post-treatment, theinventors also performed MTS assay to measure cell viability and foundthat shRNA-treated cells had approximately 20% reduced viabilityrelative to No RNAi- or miRNA-treated cells (FIG. 32). Similar toxicitywas observed at a 10-fold lower dose of shSCA1 (data not shown). Ofnote, the observed toxicity is not attributable to silencing endogenousmouse SCA1 in the C2C12 cells, as these RNAi sequences are specific forhuman SCA1.

Safety of Hairpin-Based RNAi Vectors in Mouse Cerebellum

Next, the inventors sought to test whether miRNA-based strategies showimproved safety over shRNAs in vivo. The inventors focused their effortson the cerebellum. They generated adeno-associated viral vectors (AAVserotype 2/1—FIG. 33A) expressing U6-driven shSCA1 or miSCA1. The AAVvectors also contain a hrGFP expression cassette for observing thedistribution and types of cells transduced. Wild-type mice were injectedwith AAV1-hrGFP, AAV1-shSCA1, or AAV1-miSCA1 into the cerebellum andsacrificed 10 weeks later. Immunohistochemical analyses were performedfor calbindin, which labels Purkinje cells within the molecular layer ofthe cerebellum. The inventors found that shSCA1 caused markedneurotoxicity, as evidenced by a clear loss of Purkinje cells intransduced (GFP-positive) regions of the cerebellum (FIG. 33B,C).Conversely, AAV1-hrGFP- and AAV1-miSCA1-treated cerebella showedpreserved integrity of Purkinje cells in transduced and untransducedregions (FIG. 33B,C and data not shown). These results support thatartificial miRNA expression in mouse cerebellum is well-tolerated,particularly when compared to the corresponding toxic shRNA.

Artificial miRNA-Mediated Silencing of a Therapeutic Target in PurkinjeCells

Previously the inventors found that shRNAs are more potent thanartificial miRNAs when targeting co-transfected luciferase reporters orendogenous mRNAs in HEK293 cells. However, the present in vitro and invivo safety analyses support the use of artificial miRNAs for developingvector-based RNAi therapeutics. As such, the inventors tested whetherthe potency of an artificial miRNA, miSCA1, is sufficient to silence itstherapeutic target in a mouse model of spinocerebellar ataxia type I(SCA1) which expresses a mutant human ataxin-1 transgene via aPurkinje-cell specific promoter. SCA1 is a dominantly-inheritedneurological disease which causes degeneration primarily in cerebellarPurkinje cells. The mutation responsible for the disease produces atoxic, polyglutamine-expanded form of ataxin-1, the SCA1 gene product,which localized to the nucleus.

Here, the inventors tested the capacities of the corresponding shSCA1and miSCA1 vectors to silence the mutant human ataxin-1 transgene inSCA1 mice. Mice were injected with AAV1-shSCA1 or AAV1-miSCA1 into thecerebellum and histological analyses were performed seven weeks later toevaluate viral transduction (hrGFP), Purkinje cell integrity (calbindin)and gene silencing (ataxin-1). These analyses demonstrate that treatmentwith AAV1-miSCA1 effectively silences the SCA1 therapeutic target inPurkinje cells, as evidenced by a loss of nuclear ataxin-1 staining inregions positive for both hrGFP and calbindin. Conversely, shSCA1expression caused neurotoxicity in SCA1 mice to a similar extent aspreviously observed in wild-type mice. The resulting loss ofcalbindin-positive Purkinje cells in shSCA1-treated cerebella likelyexplains the absence of ataxin-1 staining in these regions. Theseresults demonstrate that artificial miRNAs are capable of silencing acandidate target for RNAi therapy in mouse cerebellum and provideadditional support for the improved safety profile of artificial miRNAsover shRNAs.

Discussion

Here, the inventors demonstrate how the improved potency of shRNAs maybe offset by toxicity issues. High levels of RNAi substrates produced byshRNA-expression vectors saturate cellular RNAi machinery, thusinterfering with miRNA biogenesis and function in cell culture and invivo. The present findings show that miRNA-based strategies are lessprone to interfering with these processes in vitro, suggesting thatartificial miRNAs may be less toxic. The inventors extend these findingsto show that the shRNA-mediated interference occurs primarily at thelevel of miRNA biogenesis, though interference with the RISC is alsoprobable. Furthermore, the inventors demonstrate that artificial miRNAexpression may not disrupt cellular processes (i.e., myotube elongation)regulated by endogenous miRNAs nor cause cell death as compared to theircorresponding shRNAs.

In vivo, shRNAs may cause toxicity in mouse striatum independent of HDhmRNA silencing. Similar to our work, others have observed acute livertoxicity and mortality in mice following systemic shRNA delivery (Grimmet al., 2006, Nature 441, 537-41). Importantly, this toxicity correlatedwith increased mature antisense RNA levels. However, there are importantdifferences between our findings. First, Grimm et al. found thatlowering the vector dose by approximately 10-fold significantly improvedthe lethal effects of some shRNAs on liver function and animalviability. In the present studies, reducing the dose led to lowertransduction throughout the striatum, but did not abrogate toxicity.Second, the data by Grimm and colleagues show significant build-up ofshRNA precursors in liver cells. They attributed the liver toxicity, inpart, to disruption of endogenous miRNA biogenesis caused by shRNAsaturation of RNAi nuclear export machinery. In the present work, theinventors detected abundant levels of unprocessed shRNAs in vitro, butinterestingly, low to undetectable levels in vivo. This suggests thatnuclear export was likely not limiting in the present studies.Alternatively, the striatal toxicity may be caused by excessive levelsof mature antisense RNAs mediating off-target silencing of unintendedmRNAs with partial complementarity.

Although understanding the mechanism of shRNA-induced toxicity in mousestriatum is important, the inventors focused on pursuing alternativeRNAi strategies to alleviate the toxicity. They found that moving theHD2.4 and HD2.4mis sequences, both of which caused toxicity in thecontext shRNAs, into a miRNA scaffold significantly reducedneurotoxicity within the striatum with no sacrifice in gene silencingefficacy. The inventors correlated this positive effect to lowersteady-state levels of mature antisense RNAs processed from theartificial mi2.4 relative to sh2.4. Whether this disparity in expressionlevels results from differences in transcription or stability betweenshRNAs and artificial miRNAs remains to be elucidated.

The improved safety profiles of miRNA-based RNAi strategies areexciting, particularly since in vivo gene silencing efficacy was notcompromised relative to optimized shRNAs. These results support that wehave saturated gene silencing on a per cell basis, as more antisense RNAdid not increase silencing efficacy. Antisense RNA levels on a per cellbasis may be further limited by adjusting the RNAi expression and viraldelivery strategies. Conveniently, miRNA-based vectors are more amenableto Pol-II mediated transcription as compared to shRNAs, which havelimited spacing flexibility for Pol-II based expression. ArtificialmiRNAs more naturally resemble endogenous RNAi substrates and are moreamenable to Pol-II transcription (allowing tissue-specific expression ofRNAi) and polycistronic strategies (allowing delivery of multiple siRNAsequences). This advantage allows for regulated and cell-specificexpression of inhibitory RNAs. These versatile expression strategiesenhance the application of as biological tools and may further limitpotential toxicity in therapeutic applications. For these reasons, inaddition to the present findings, artificial miRNAs are more suitablefor the development of vector-based RNAi therapeutics.

Material and Methods

Vectors

Plasmids expressing U6-driven artificial miRNAs or shRNA vectorstargeting SCA1 have been previously described along with the SCA1 andGFP RNAi luciferase reporter plasmids. The miR-1 Firefly luciferasereporter was cloned using a similar strategy. Briefly, a single sitewith perfect complementarity to miR-1 was inserted into the 3′UTR ofFirefly luciferase (psiCheck™2, Promega®) using a tailed-PCR strategywith the following primers:forward—5′-AAAATCTAGATACATACTTCTTTACATTCCACCGCTTCGAGCAGACATG-3′ (SEQ IDNO:213), reverse—5′-AAAAGGATCCTCGAGCGATTTTACCACATTTGTAGAGG-3′ (SEQ IDNO:214). This PCR product was digested with XbaI-BamHI and cloned intothe same sites within psiCheck™2. For C2C12 and AAV vector production,miRNA or shRNA expression cassettes driven by the mouse U6 promoter werecloned into a derivative of the pFBGR plasmid upstream of aCMV-hrGFP-SV40 polyA expression cassette.

In Vitro Luciferase Assays

HEK293 cells grown in black 96-well plates (Costar 3603; Corning Inc.)were co-transfected in triplicate with RNAi-expressing plasmids (10 to100 ng) and RNAi luciferase target plasmids (10 to 20 ng). In dosingstudies, empty-vector was supplemented to low doses to match total DNAload. Firefly and Renilla luciferase activities were assessed 24 hpost-transfection using the Dual-Glo Luciferase Assay System (Promega®)per manufacturer's instructions, using 50 μl per substrate. Luminescentreadings were acquired with a 96-well plate luminometer (Dynex). Resultswere calculated as the quotient of Renilla/Firefly luciferaseactivities.

For C2C12 studies, cells grown in 24-well plates coated withpoly-1-ornithine (0.1 mg/ml, Sigma) were transfected in quadruplicatewith 200 ng of endotoxin-free RNAi or empty-vector plasmids along with40 ng of siCheck™2 or miR-1 luciferase reporter (target site in 3′UTR ofFirefly luciferase) plasmids. Cells were differentiated byserum-starvation at 4 h post-transfection, and Dual Luciferase assays(Promega®) were performed 48 h later with a 96-well plate luminometer(Berthold Technologies). Of note, undifferentiated samples wereharvested at 24 h post-transfection as cells were nearing 100%confluence. Results were calculated as the quotient of Firefly/Renillaluciferase activities.

Northern Blot Analyses

HEK293 cells grown in 6-well plates were transfected with RNAi plasmids(0.2 or 2 μg SCA1 RNAi with 1.5 μg miGFP for competition studies or 0.2or 2 μg HD2.4 RNAi). Empty-vector plasmid was supplemented to low dosesto match total DNA load. Total RNA was isolated at 48 hpost-transfection using 1 ml TRIzol® reagent (Invitrogen™), and 15-20 μgwas resolved on a 15% acrylamide gel. Small transcript sizes weredetermined with the Decade Ladder (Ambion®). Loading was assessed byethidium bromide stain. RNA was transferred to Hybond™-XL membrane(Amersham) and UV-crosslinked. Blots were pre-hybridized usingUltraHyb®-Oligo (Ambion®) at 35° C., probed with γ-³²P-labeledoligonucleotides (Ready-To-Go T4 polynucleotide kinase; Amersham) at30-35° C. overnight, washed in 2×SSC, 0.1% SDS at 30-35° C., and exposedto film.

For in vivo studies, total RNA from striatal tissue punches washarvested using 1 ml TRIzol® reagent (Invitrogen™). Northern blots wereperformed as indicated above using 1-3 μg RNA.

C2C12 Elongation Analyses

C2C12 cells grown in 24-well plates coated with poly-1-ornithine (0.1mg/ml) were transfected with 200 ng of empty-vector or RNAi plasmidsco-expressing hrGFP and differentiated after 4 h. At 72 h, cells werewashed twice with PBS and fixed in 4% formaldehyde forimmunocytochemistry (done at room temperature). Alternatively,undifferentiated cells were fixed at 24 h post-transfection. Fixed cellswere incubated in blocking buffer (2% bovine albumin, 2% horse serum,0.1% NP-40 in PBS) for 30 min. Anti-myosin heavy-chain (MHC) primaryantibody (1:1000, MF20 from the University of Iowa Hybridoma Facility)was added with fresh blocking buffer and incubated for 2 h. Cells werethen washed twice with PBS, incubated with an Alexa-568-conjugatedanti-mouse IgG (1:5000, Invitrogen™) for 30 min, and washed again withPBS. Fluorescence microscopy images (red-MHC and green-hrGFP) werecaptured at 10× magnification using an Olympus IX70 (microscope) andDP70 (camera) coupled with Olympus DP Controller software. Correspondingimages were overlayed, and the lengths of GFP+/MHC+ cells werequantified using Image J software (NIH).

C2C12 Survival Studies

Cells grown in 24-well plates coated with poly-1-ornithine (0.1 mg/ml)were transfected in triplicate with 400 ng of endotoxin-freeempty-vector or RNAi plasmids co-expressing hrGFP and differentiatedafter 4 h. At 24 h and 72 h post-transfection, fluorescence microscopyimages were captured at 4× magnification using an Olympus IX70(microscope) and DP70 (camera) coupled with Olympus DP Controllersoftware. At 72 h, cells were trypsinized, resuspended in 1 ml of growthmedia, and 100 μl aliquots (in triplicate) were analyzed using theCellTiter-96 AQueous MTS assay (Promega®) per manufacturer'sinstructions. Absorbance was measured with a 96-well microplate reader(Molecular Devices) and normalized to cells treated with empty-vector.

Viral Vector Production and Purification

Recombinant AAV vectors were produced by a standard calcium phosphatetransfection method in adherent HEK293 cells, using the Ad helper,trans-packaging and AAV vector plasmids as previously described. Vectortiters were determined by QPCR, using a Prism 7900 sequence detector(Applied Biosystems), and were between 3 and 10×10¹² DNase-resistantparticles (DRP)/ml (later referred to as viral genomes/ml). Viralinfectivity was assessed in a TCID50 assay using the HeLa-based B50 cellline. AAV1.mi2.4, AAV1.mi2.4mis, AAV1.sh2.4 and AAV1.GFP were producedby Targeted Genetics Incorporated, and AAV1.miSCA1 and AAV1.shSCA1 wereprovided by the University of Iowa Vector Core facility.

AAV Injections

All animal protocols were approved by the University of Iowa Animal Careand Use Committee. Eight-week old C57/BL6 mice (Jackson Laboratories)were injected with AAV2/1-expressing shRNAs or miRNAs and sacrificed 16weeks later. Mice were anesthetized with xylazine (100 mg/kg) andketamine (10 mg/kg), their heads shaved, sterilized with betadine andplaced in a Kopf stereotaxic frame specially adapted for mouse surgery.A midline incision was made and unilateral burr holes were created overthe right striatum with a high-speed dental drill. Subsequently, 5 μl ofeither AAV1.sh2.4, AAV1.mi2.4 or AAV1.mi2.4mis (4×10¹² viral genomes/ml)was injected into the right striatum (coordinates: 0.86 mm rostral tobregma, 1.8 mm lateral to midline, 3.5 mm ventral to the skull surface).All injections were performed through a 10 μl Hamilton syringe connectedto an infusion pump at a rate of 0.2 μl/min with a 33-gauge, blunttipped needle. The needle was left in situ for an additional 5 min toallow the injectate to diffuse from the needle tip. The scalp was closedwith 5-0 polyvicryl suture. For cerebellar studies in SCA1 mutant mice,1 μl of either AAV1.shSCA1 or AAV1.miSCA1 (1×10¹² viral genomes/ml) wasinjected into the cerebellum (coordinates: 6.0 mm caudal to bregma, 2.0mm lateral to midline, 1.0 mm ventral to the skull surface) as describedabove using a Hamilton syringe cemented with a glass micropipette tip.

Sacrifice

Mice used in histological analyses were anesthetized with aketamine/xylazine mix and transcardially perfused with 20 ml of 0.9%cold saline, followed by 20 ml of 4% paraformaldehyde in 0.1M PO₄buffer. Mice were decapitated, the brains removed and post-fixedovernight. Brains were stored in a 30% sucrose solution at 4° C. untilcut on a sliding knife microtome at 40-μm thickness and stored at −20°C. in a cryoprotectant solution. Mice used for biochemical analysis wereperfused with 20 ml of 0.9% cold saline. Brains were removed andsectioned into 1 mm thick coronal slices using a brain matrix (Roboz).Tissue punches were taken from the striatum using a tissue core (1.4 mmin diameter) and triterated in 50 μl of TRIzol (Invitrogen™).

Quantitative Real-Time PCR (QPCR)

For in vitro studies, HEK293 cells grown in 24-well plates weretransfected with 700 ng of HD2.4 RNAi expression plasmids and cellsharvested 48 h later. RNA was isolated from HEK293 cells or striataltissue punches using 1 ml of TRIzol reagent (Invitrogen™). Random-primedfirst-strand cDNA synthesis was performed using 500 ng total RNA(TaqMan® reverse transcription reagents; Applied Biosystems) permanufacturer's protocol. Assays were performed on a sequence detectionsystem using primers-probe sets specific for human HD and GAPDH or mouseHDh, CD11b (Itgam) and β-actin (Prism 7900HT and TaqMan® 2× UniversalMaster Mix; Applied Biosystems). Relative gene expression was determinedby using the ΔΔC_(T) method, normalizing to either GAPDH or β-actin mRNAlevels.

Immunohistochemical Analyses

Free-floating, coronal brain sections (40 μm thick) were processed forimmunohistochemical visualization of striatal neurons (DARPP-32, 1:100,Cell Signaling Technology), microglia (Iba1, 1:1000, WAKO), cerebellarPurkinje cells (Calbindin, 1:2000, Cell Signaling Technology), or mutanthuman ataxin-1 (11NQ). Sections were first incubated in 0.1 M sodiumperiodate in Tris-buffered saline (TBS) for 20 min to remove endogenousperoxidase activity and then blocked with 5% normal goat serum for 1 h.After blocking, sections were incubated with primary antibody for 24 h,washed, and then incubated with biotin- or Cy3-labeled goat anti-rabbitIgG secondary antibodies (1:200, Vector Laboratories and JacksonImmunoresearch) for 1 h. Sections were washed again and placed inVectastain ABC-peroxidase reagent (Vector Laboratories) for 1 h.Sections were then washed and incubated in a chromagen solutioncontaining 0.05% 3,3′-diaminobenzidine tetrahydrochloride and 0.005%hydrogen peroxidase for up to 5 min. All staining procedures werecarried out at room temperature and deletion of the primary antibodyserved as a control. Sections were mounted onto Superfrost™ Plus slides(Fisher Scientific) and coverslipped with Gelmount (Biomeda). Imageswere captured using an Olympus BX60 light microscope and DP70 digitalcamera, along with Olympus DP Controller software.

Statistical Analyses

Student's t-Test was used for all studies, unless indicated otherwise.For C2C12 elongation analyses, a one-way analysis of variance (ANOVA)was performed followed by Bonferroni post-hoc analyses to assess forsignificant differences between individual groups. In all statisticalanalyses, P<0.05 was considered significant.

Vector Design

An expression cassette (5′NheI-3′BglII) containing the CMV promoter,multiple cloning site (MCS) and SV40 polyadenylation (polyA) signal wascloned into TOPO-BluntII (XbaI-BamHI, Invitrogen™) in reverseorientation. A Pol-III expression cassette containing mouse U6 promoter,MCS and Pol-III-terminator (6T's) was cloned into TOPO-BluntII with thesame strategy. Artificial miRNAs were generated by polymerase extensionof overlapping DNA oligonucleotides (IDT). Polymerase-extended productswere digested with XhoI-SpeI and cloned into the MCS of the expressionvectors XhoI-SpeI (miV1) or XhoI-XbaI (miV2). miV3 resulted from anunexplained cloning error. Other shRNAs were cloned using a tailed-PCRstrategy. PCR products containing U6-shRNA-6T's were TOPO cloned intothe BluntII vector and positive clones were considered to be in reverseorientation to maintain consistency with the other expression vectors.

For in vivo studies, miRNA or shRNA expression cassettes driven by themouse U6 promoter were cloned in the same orientation upstream of aCMV-hrGFP-SV40polyA expression cassette.

RNAi luciferase reporter vectors were constructed using psiCheck2™(Promega®). Tailed-PCR was used to amplify a 3′ fragment of Renillaluciferase containing a single, perfect complementary RNAi target site(˜25-bp: 21-bp target+2-nt 5′ and 3′) downstream of the stop codon. ThisPCR product was digested with AatII-XhoI and cloned into the same siteswithin psiCheck™2.

See FIG. 31 for detailed information about vector construction.

Northern Blot Analyses

HEK293 cells grown in 6-well plates were transfected with 1.5 μg of RNAiexpression plasmid. Total RNA was isolated at 48 h post-transfectionusing 1 ml TRIzol® reagent (Invitrogen™); alternatively, the small RNAfraction was harvested using mirVana™ Isolation Kit (Ambion®). 15-20 μgtotal RNA or 1-2 μg small RNA fraction was resolved on a 15% acrylamidegel. Small transcript sizes were determined with the Decade Ladder(Ambion®). Consistent loading and RNA integrity was assessed by ethidiumbromide stain. RNA was transferred to Hybond-XL membrane (AmershamPharmacia) at 200-400 mA for 1-2 h and UV-crosslinked with theauto-crosslink function on a Stratalinker 1800 (Stratagene®). Blots werepre-hybridized using UltraHyb-Oligo (Ambion®) at 35° C., probed with³²P-labeled oligonucleotides (Ready-To-Go T4 polynucleotide kinase;Amersham) at 30-35° C. overnight, washed three times (5 min each) in2×SSC, 0.1% SDS at 30-35° C., and exposed to film. Alternatively, blotswere probed with biotin-labeled oligonucleotides and analyzed using theBio-Detect Kit (Ambion®). Densitometry analyses were performed using abioimaging system (UVP) coupled with LabWorks software (UVP).

Quantitative Real-Time PCR Analyses

HEK293 cells grown in 24-well plates were transfected with 700 ngRNAi-expressing plasmids. At 48 h post-transfection, total RNA wasisolated with 0.5 ml TRIzol® reagent (Invitrogen™), and random-primedfirst-strand cDNA synthesis was performed using 1 μg total RNA (TaqMan®reverse transcription reagents; Applied Biosystems) per manufacturer'sprotocol. Assays were performed on a sequence detection system usingprimers-probe sets specific for human HD, SCA1, GAPDH or 18S rRNA (Prism7900HT and TaqMan 2×Universal Master Mix; Applied Biosystems). Relativegene expression was determined by using the relative standard curvemethod.

GFP Silencing Analyses

HEK293 cells grown in 12-well plates were transfected with 1.2 μg and300 ng of RNAi (SCA1 or GFP) and eGFP expression plasmids respectively.At 48 h post-transfection, fluorescent photomicrographs were captured at4× magnification using an Olympus IX70 (microscope) and DP70 (camera)coupled with Olympus DP Controller software. Mean fluorescence in eachimage was determined using the histogram function in Image J software(NIH). Results for GFP RNAi-treated cells were normalized to controlSCA1 RNAi-treated cells.

In Vitro Luciferase Assays

HEK293 cells grown in black 96-well plates (Costar 3603; Corning Inc.)were co-transfected in triplicate with RNAi-expressing plasmids (1-60ng) and RNAi luciferase target plasmids (10-20 ng). In dosing studies,empty-vector was supplemented to low doses to match total DNA load.Firefly and Renilla luciferase activities were assessed 24 hpost-transfection using the Dual-Glo Luciferase Assay System (Promega®)per manufacturer's instructions, using 50 μl per substrate. Luminescentreadings were acquired with a 96-well plate luminometer (Dynex). Resultswere calculated as the quotient of Renilla/Firefly luciferaseactivities.

In Vivo Luciferase Assays

Animal studies were approved by the University of Iowa Animal Care andUse Committee. Eight-week old male C57/BL6 mice (Jackson Laboratories)were anesthetized with ketamine-xylazine and injected with 30 μl of 0.4U/μl hyaluronidase (Sigma) into the tibialis anterior (TA) muscle. Twohours later, plasmids in 30 μl saline were injected into the TA muscleof re-anesthetized mice were. All groups (n=4 muscles) received 1 μgRNAi luciferase reporter plasmid along with 10 μg empty vector or RNAiplasmid (high dose) or 9 μg empty vector and 1 μg RNAi plasmid (lowdose). Plasmids were prepared using the EndoFree® Plasmid Maxi Kit(Qiagen). Plasmid-injected muscles were electroporated as previouslydescribed applying 175 V/cm in 10 20 ms pulses at 2 Hz (ECM 830electroporator, BTX). At 4 and 8 d days post-treatment, mice weresedated with isoflurane, and 30 μl of coelenterazine (0.3 mg/ml,Promega®) was injected into the TA muscles. Bioluminescence imaging wasperformed immediately using an IVIS200 imaging system (Xenogen). Lightemissions were analyzed using Living Image software (Xenogen) and IgorPro image analysis software (WaveMetrics Inc.). Data collected at 4 and8 d revealed similar silencing trends (4 d not shown).

Statistical Analyses

Student's t-Test was used for all studies where P-values are provided.In all statistical analyses, P<0.05 was considered significant.

EXAMPLE 6 Artificial miRNAs Mitigate shRNA-Mediated Toxicity in theBrain: Implications for the Therapeutic Development of RNA Interference

The ability of small interfering RNAs (siRNAs) to silence target geneswas first demonstrated in 1998 and has since emerged as a revolutionarystrategy to reduce target gene expression. RNAi occurs naturally incells as a post-transcriptional regulatory mechanism mediated byendogenous miRNAs. RNAi is hypothesized to have evolved as a cellularcoping mechanism providing the cell a means to decrease the expressionof various deleterious viruses and transposons. In recent years,scientists have co-opted this biological process to reduce expression oftarget mRNAs using exogenously applied siRNAs, shRNAs or artificialmiRNAs. Aside from the widespread basic biological applications of RNAi,the ability to reduce gene expression marks a major advance towards thedevelopment of disease therapies, particularly for dominantly inheriteddisorders.

Among the dominant diseases that may benefit from RNAi-based therapiesis Huntington's disease (HD). Partial reduction of mutant huntingtinexpression by viral delivery of shRNAs is efficacious in preventing thedevelopment of motor deficits and neuropathology in transgenic mousemodels of HD. In proof-of-principal studies, the therapeutic effect ondisease phenotype was studied by knocking down a mutant human HDtransgene in the setting of two normal mouse HDh alleles. Whileallele-specific targeting of disease transcripts for HD therapy would beideal, to date, no prevalent single nucleotide polymorphism (SNP)residing on the mutant transcript has been identified. Therefore, theinventors undertook studies to identify inhibitory RNAs that wouldtarget both mouse HDh and human HD transcripts, with the intention oftesting the efficacy of reducing expression of both alleles in aknock-in model of HD. This example describes the surprising finding ofneurotoxicity in mouse brain caused by some, but not all, shRNAexpression vectors screened in vivo, and the notable reduction intoxicity after moving those toxic inhibitory RNAs into miRNA-baseddelivery systems.

Results

shRNAs Cause Striatal Toxicity in Mice

First shRNAs (driven by the mouse U6 promoter) that target conservedsequences spanning human HD and mouse HDh mRNAs were designed andscreened (FIGS. 34 and 35A). Silencing of HD mRNA measured byquantitative real-time PCR (QPCR) and dot blot analysis revealed adecrease in huntingtin protein expression following transfection ofshRNA expression plasmids into mouse C2C12 and human-derived HEK293 celllines (data not shown). Of the 35 shRNAs tested, 3 were chosen forfurther study based on silencing efficacy. The shRNAs target sequencesin exons 2, 8 and 30 of HD mRNAs, and are henceforth referred to assh2.4, sh8.2 and sh30.1, respectively (FIG. 35B). Western blot analysisdemonstrated that these shRNAs, but not mismatch (mis) control shRNAs,reduce endogenous huntingtin protein expression in mouse C2C12 cells(FIG. 35C). Similar results were seen in human-derived HEK 293 cells.

To examine the long-term effects of brain-delivered shRNAs in the CAG140knock-in mouse model, U6-shRNA expression cassettes were cloned intoadeno-associated viral vectors (AAV serotype 2/1—FIG. 36A). AAVs alsocontained a humanized Renilla green fluorescence protein (hrGFP)expression cassette to identify the distribution and types of cellstransduced. Five-week old CAG140 knock-in mice were injected bilaterallyinto the striatum with AAVsh2.4-GFP, AAVsh8.2-GFP, AAVsh30.1-GFP orAAV-GFP (viral control) and sacrificed 15 weeks later. Robust expressionof GFP was observed in cells throughout the rostral/caudal extent of thestriatum and within fibers of the globus pallidus (FIG. 36B).Immunofluorescence analyses indicated that GFP-positive cellsco-localized with a neuronal marker (NeuN) but not with markers forastrocytes (GFAP) or oligodendrocytes (RIP1) (FIG. 37). QPCR performedon RNA isolated from GFP-positive striatal tissue showed a significantand statistically similar reduction of HDh mRNA expression (˜60%) amongthe different active shRNA-expressing vectors compared to mice injectedwith AAV-GFP (FIG. 36C, F(3,11)=32.3, P<0.001 for post-hoc analysescomparing each AAV-shRNA group to the AAV-GFP control). Moreover,western blot analysis demonstrated a significant reduction in huntingtinprotein levels following AAVshRNA-GFP administration compared tocontrols (FIG. 37, t(8)=3.9, P<0.01).

Unexpectedly, immunohistochemical analyses for dopamine- andcAMP-regulated protein (DARPP-32), a marker of medium-sized spinyprojection neurons in the striatum, revealed striatal toxicity in miceinjected with AAVsh2.4-GFP and AAVsh30.1-GFP (FIG. 36D, top panel).Reduction in DARPP-32 immunoreactivity was largely confined to thetransduced (GFP-positive) regions of the striatum. Interestingly, thistoxicity was not seen in mice injected with AAVsh8.2-GFP (FIG. 36D, toppanel); striata from these mice were similar to AAV-GFP-injected controlmice.

To assess whether the observed loss of DARPP-32 staining was associatedwith microglial activation, tissue sections were stained with ananti-Iba1 antibody to identify both resting and reactive microgliathroughout the brain. AAVsh2.4-GFP and AAVsh30.1-GFP-injected striatademonstrated high Iba1 expression, whereas AAVsh8.2-GFP-injected striatawere similar to control mice (FIG. 36D, bottom panel). Moreover,AAVsh2.4-GFP- and AAVsh30.1-GFP-injected mice demonstrated dramaticreactive astrogliosis compared to AAVsh8.2-GFP and control-injectedmice, as evidenced by robust GFAP staining in areas of the striatumcorresponding to high GFP positivity (data not shown). Notably, amismatch control for the 2.4 sequence, AAVsh2.4mis-GFP, induced toxicitysimilar to sh2.4 and sh30.1, without reducing HDh mRNA expression. This,in addition to the sh8.2 data, indicates that three (two active, oneinactive) of four shRNAs were toxic and that toxicity is not caused bysilencing huntingtin.

Although all U6-shRNA expression cassettes were cloned into the sameviral vector, the inventors tested for the possibility that toxicitycorrelated with steady-state levels of the expressed products. RNAsamples harvested from shRNA-treated striata were analyzed by smalltranscript northern blot probing for the mature antisense (AS) and sense(S) RNAs generated by the respective shRNAs. Results demonstrate thatsh2.4 AS RNA and sh30.1AS RNA are expressed more robustly than sh8.2 ASRNA (n=2 per group, FIG. 38), thus correlating toxicity with increasedexpression levels of the shRNAs in vivo. The disparity in expressionlevels is interesting, particularly given the fact that each shRNA wasdesigned using the same rules, injected at the same viral dose, drivenby the same Pol-III promoter and silenced HDh mRNA to a similar degree.Notably, the sense strands and pre-processed products for the shRNAswere not detectable in brain lysates, suggesting that the toxicity isdue, in part, to high levels of inhibitory RNAs rather thaninappropriate sense strand loading into the RNA-induced silencingcomplex (RISC).

Artificial miRNAs are Expressed at Lower Levels Relative to shRNAs

Because the toxic shRNAs were expressed at higher levels than thenon-toxic, active hairpin, an approach to reduce toxicity would be tolower the viral titer injected. In brain, decreasing the titers by ahalf log (1e¹²) or a full log (5e¹¹) achieved silencing of HDh mRNA (47%and 51%, respectively) but did not alleviate striatal toxicity (FIG.39). Decreasing the titers even further (1e¹¹ or 5e¹⁰) reduced thesilencing efficacy to 15% of controls, making it non-viable as atherapeutic (FIG. 39). Thus, the inventors tested if levels ofinhibitory RNAs could be minimized without compromising silencingefficacy using an artificial miRNA as a siRNA shuttle (versus a shRNA).

As shown in Example 4 above, artificial miRNAs effectively silencetarget gene expression relative to shRNAs, without generating excessivelevels of inhibitory RNAs. Consequently, the inventors cloned two of thetoxic sequences (HD2.4 and HD2.4mis) into an artificial miRNA scaffoldbased on human miR-30, thus creating mi2.4 and mi2.4mis (FIG. 40A).Expression levels of mi2.4 and sh2.4 were first compared by smalltranscript northern blot analysis at 48 h post-transfection ofRNAi-expressing plasmids into HEK 293 cells. Probing for the HD2.4antisense strand revealed that mi2.4 produces substantially lower levelsof inhibitory RNAs relative to sh2.4. Notably, sh2.4 generates anabundance of precursor and processed RNAs, even at a 10-fold lower dose(FIG. 40B). Despite the dramatic difference in expression levels, mi2.4reduced endogenous HD transcripts almost as effectively as sh2.4 (50%and 60% silencing, respectively) in HEK 293 cells (FIG. 40C).

Artificial miRNAs Mitigate Striatal Toxicity in Mice

Next AAV2/1-expressing mi2.4 or the mi2.4 mismatch control weregenerated (FIG. 36B, 40A) to test whether the development of striataltoxicity could be prevented relative to AAVsh2.4-GFP. BecauseshRNA-induced toxicity was not dependant on the disease model,subsequent studies were performed in wild-type mice. Mice were injectedinto the right striatum with AAVsh2.4-GFP, AAVmi2.4-GFP orAAVmi2.4mis-GFP and sacrificed 4 months post-injection. The time-course,volume and titer were identical to those used in our earlier shRNAstudies (FIG. 36). QPCR performed on RNA isolated from mouse striatashowed a statistically significant reduction of HDh mRNA (˜70%)following treatment with either sh2.4- or mi2.4-expressing vectorscompared to uninjected striata or striata treated with mi2.4mis (FIG.39A, F(2,8)=77.6, P<0.001 for post hoc analyses comparing sh2.4 andmi2.4 versus uninjected and mi2.4mis). Importantly, the degree of HDhmRNA silencing between sh2.4 and mi2.4 was similar and not significantlydifferent (P>0.05). Additional QPCR analyses were performed on thesesamples to measure CD11b mRNA, a readout for microglial activation, asan initial assessment for toxicity. Striata treated with sh2.4 showednearly a 4-fold increase of CD11b mRNA relative to uninjected striata,while mi2.4- and mi2.4mis-treated striata showed only minimal induction(FIG. 5B, F(2,8)=23.6, P<0.001 for post-hoc analyses comparing sh2.4 toall other groups). To determine if these differences in toxicity couldbe attributed to levels of HD2.4 inhibitory RNAs, the inventorsperformed northern blot analysis on the same RNA samples used for theQPCR analyses. Although silencing efficacies between the sh2.4- andmi2.4-treated groups were comparable, northern blot analysis, probingfor the HD2.4 antisense strand, demonstrated considerably more matureantisense RNAs in sh2.4-treated mice relative to mi2.4-treated mice(FIG. 39C). These results corroborate our in vitro findings andcorrelate the improvement in toxicity with reduced levels of HD2.4antisense RNA.

The inventors further assessed striatal toxicity by histologicalanalyses. Immunolabeling for DARPP-32 expression revealed significantattenuation of striatal toxicity in AAVmi2.4-GFP-injected cohortsrelative to AAVsh2.4-GFP-injected mice (FIG. 39D, middle panel).Moreover, the intense microglial activation (Iba1 positive cells) seenin AAVsh2.4-GFP-injected mice was scarcely present inAAVmi2.4-GFP-injected mice (FIG. 39D, lower panel and FIG. 41). Of note,mi2.4mis-treated brains also showed no apparent toxicity by theseanalyses, whereas, 2.4mis was toxic when delivered as a shRNA. Thus,sequences encoding HD2.4 and HD2.4mis were toxic in the setting of ashRNA in brain, but not in the context of a miRNA scaffold.

Discussion

Here, it has been show that some shRNAs cause toxicity in mouse striatumindependent of HDh mRNA silencing. Similar to the present work, Grimmand colleagues observed acute liver toxicity and mortality in micefollowing systemic shRNA delivery, which correlated with increasedmature antisense RNA levels (Grimm et al., 2006, Nature 441, 537-41).However, there are important differences between the present findings.First, Grimm et al. found that lowering the vector dose by approximately10-fold significantly improved the lethal effects of some shRNAs onliver function and animal viability. In the present studies, reducingthe dose led to lower transduction throughout the striatum, but did notabrogate toxicity. Second, the data by Grimm and colleagues showsignificant build-up of shRNA precursors in liver cells. They attributedthe liver toxicity, in part, to saturation of endogenous RNAi exportmachinery. In the present work, the inventors detected abundant levelsof unprocessed shRNAs in vitro, but interestingly, low to undetectablelevels in vivo. This suggests that export was likely not limiting in thepresent studies. Alternatively, the striatal toxicity may be caused bythe build-up of antisense RNAs and subsequent off-target silencing ofunintended mRNAs. The present data on sh8.2 is also consistent withthis; sh8.2 was not toxic when delivered at the same dose as sh2.4 andsh30.1. And though silencing activity was similar between the threeshRNAs, levels of mature product for sh8.2 was significantly lower.

The inventors found that moving the HD2.4 and HD2.4mis sequences, bothof which caused toxicity in the context of a shRNA, into a miRNAscaffold significantly reduced neurotoxicity within the striatum with nosacrifice in gene silencing efficacy. The inventors correlated thispositive effect to lower steady-state levels of mature antisense RNAsprocessed from the artificial mi2.4 relative sh2.4. Whether thisdisparity in expression levels results from differences in transcriptionor stability between shRNAs and artificial miRNAs remains unknown.However, the latter provides a more likely explanation since sh2.4 andmi2.4 are expressed from the same mouse U6 promoter and only differ insize by approximately 100 nucleotides.

In addition to improved safety profiles, artificial miRNAs are amenableto Pol-II mediated transcription. Conversely, shRNAs have limitedspacing flexibility for expressing shRNAs from Pol II based promoters.This advantage of miRNA-based systems allows for regulated andcell-specific expression of inhibitory RNAs. These versatile expressionstrategies advance the application of artificial miRNAs as biologicaltools and may further limit potential toxicity in therapeuticapplications.

In some diseases, it is possible to specifically target disease-linkedSNPs that exist on the mutant transcript. For HD however, no prevalentSNP has been reported. Because earlier work showed that a minimum of 50%huntingtin expression is required to offset the embryonic lethalitynoted in huntingtin null mice, knowing the consequences of reducinghuntingtin expression in adult brain is important to moving non-allelespecific RNAi forward as a HD therapy. The present data with sh8.2 andmi2.4 are encouraging, and suggests that the mammalian brain cantolerate greater than 50% reduction in HD mRNA for 4 months, the lasttime point studied. The long-term safety and efficacy of sh8.2 iscurrently being tested in a study including histochemical, biochemicaland behavioral readouts in CAG140 HD mice.

In summary, the present experiments show that reducing HDh mRNA levelsin adult mammalian brain is tolerated. The inventors also make theimportant observation that the toxicity of shRNAs following theirexpression in brain is alleviated by moving the inhibitory RNA sequencesinto an artificial miRNA scaffold. Thus, miRNA-based approaches are moresuitable for achieving RNAi in brain to address basic research questionsor develop disease therapies.

Materials and Methods

Expression Vectors and AAV

shRNA expression cassettes were generated by PCR and cloned intopCR-Blunt-II TOPO vectors (Invitrogen™). Each candidate shRNA expressioncassette consisted of a mouse U6 promoter, an shRNA that targetshuntingtin sequences, mismatch control sequences containing fourbase-pair changes relative to the respective huntingtin shRNAs or E.coli β-galactosidase (shLacZ) and an RNA polymerase III terminationsequence (six thymidine nucleotides). For artificial miRNAs, siRNAssequences based on HD2.4 or HD2.4mis were embedded into an artificialmiRNA scaffold comparable to human miR-30, to generate mi2.4 andmi2.4mis (general structure shown in FIG. 4A). The artificial miRNAstem-loops were cloned into a mouse U6 expression vector so that greaterthan 30 nucleotides (5′ and 3′) flank the stem-loop in the transcribedproduct.

AAV shuttle plasmids pAAVsh2.4-GFP, pAAVsh2.4mis-GFP, pAAVsh8.2-GFP,pAAVsh30.1-GFP, pAAVmi2.4-GFP and pAAVmi2.4mis-GFP contain therespective RNAi expression cassettes driven by the mouse U6 promoter.The AAV shuttles also contained a humanized Renilla GFP (hrGFP) geneunder the control of the human cytomegalovirus immediate-early geneenhancer/promoter region, a chimeric human β-globin eGFP expressioncassette followed by the splice donor/human immunoglobulin spliceacceptor site, and a bovine growth hormone poly (A) signal. Thesetranscriptional units are flanked at each end by AAV serotype 2 145-bpinverted terminal repeat sequences. The trans-packaging plasmids,pBSHSPR2C1, were constructed as follows: genomic DNA was extracted fromAAV1 (American Type Culture Collection) and the cap coding sequence wasamplified by PCR using Pfx polymerase (Invitrogen™). The AAV2 cap genewas excised from the AAV2 helper plasmid pBSHSPRC2.3 and replaced withthe amplified AAV1 cap sequence using a Swa I restriction site in therep/cap intergenic junction and a BsrG I site engineered just upstreamof the AAV2 poly(A) signal. The resulting trans-packaging construct,pBSHSPR2C₁, contains the AAV2 rep gene under the control of a minimaleukaryotic promoter, and the AAV1 cap ORF positioned between the AAV2rep/cap intergenic junction and the AAV2 poly(A) signal. The plasmid pAdHelper 4.1 expresses the E2a, E4-orf6 and VA genes of adenovirus type 5(Ad5) for AAV amplification.

Recombinant AAV vectors were produced by a standard calcium phosphatetransfection method in HEK 293 cells, using the Ad helper,trans-packaging and AAV shuttle plasmids. Vector titers were determinedby real-time PCR and were between 5 and 20×10¹² DNase-resistantparticles (DRP)/mL. Vector infectivity was assessed in a TCID50 assayusing the HeLa-based B50 cell line.

Animals

All animal protocols were approved by the ACUCA at the University ofIowa. CAG140 heterozygous knock-in mice and wildtype littermates werebred and maintained in the animal vivarium at the University of Iowa.Mice were genotyped and repeat length identified by separate PCRreactions using primers flanking the CAG repeat. Mice were housed ingroups of either two or three per cage and in a controlled temperatureenvironment on a 12 hour light/dark cycle. Food and water were providedad libitum.

AAV Injections

CAG140 knock-in or wildtype mice were injected with AAVshRNAs orAAV-miRNAs (at the indicated titer) at 5 wk of age and sacrificed at 4months post-injection. Procedures were as follows: in the initial study,5 μl injections of either AAVsh2.4GFP, AAV30.1sh-GFP, AAVsh8.2-GFP orAAV-GFP were made bilaterally into striata (coordinates: 0.86 mm rostralto bregma, ±1.8 mm lateral to midline, 3.5 mm ventral to the skullsurface). For the miRNA/shRNA comparison study, 5 μl injections ofvector were injected unilaterally. Injection rates for all studies were0.2 μl/min. Mice used in histological analyses were anesthetized with aketamine/xylazine mix and transcardially perfused with 20 ml of 0.9%cold saline, followed by 20 ml of 4% paraformaldehyde in 0.1M PO₄buffer. Brains were removed, post-fixed overnight, and 40-μm thicksections collected. Mice used for molecular analyses were perfused with20 ml of 0.9% cold saline, brain removed and blocked into 1 mm thickcoronal slices. Tissue punches were taken using a tissue corer (1.4 mmin diameter). All tissue punches were flash frozen in liquid nitrogenand stored at −80° C. until used.

Molecular Studies

For in vitro shRNA screening, shRNA expression plasmids were transfected(Lipofectamine 2000, Invitrogen™) into human HEK 293 cells or mouseC2C12 cells, which naturally express full-length human or mousehuntingtin, respectively. Huntingtin levels were assessed by protein dotblot (anti-huntingtin primary antibody MAB2166, 1:5000; Chemicon) orwestern blot (protein loading control, anti-β Catenin, 1:4,000, AbCam).Knock down was also assessed by QPCR using a human huntingtin-specificTaqMan® primer/probe set with normalization to a human GAPDHprimer/probe set. This QPCR strategy was also used to evaluate HDknockdown mediated by sh2.4 and mi2.4 in FIG. 40B.

For in vivo QPCR analyses, tissue was dissected from GFP-positivestriatum and relative gene expression was assessed using TaqMan®primer/probe sets for mouse HDh, CD11b, and beta-actin. All values werequantified using the ΔΔC_(T) method (normalizing to beta-actin) andcalibrated to either AAV-GFP injected striata (screening study) oruninjected striata (miRNA-shRNA comparison study).

For northern blot analyses, tissue was dissected from GFP-positivestriatum. RNA was harvested by TRIzol® reagent (Invitrogen™) and RNA (1to 5 μg and 15 μg for in vivo and in vitro studies, respectively) wasresolved on 15% polyacrylamide/urea gels, and RNA was visualized byethidium bromide staining and UV exposure to assess loading and RNAquality. Samples were then transferred to Hybond™-N+/XL membranes(Amersham Pharmacia) and UV cross-linked. Blots were probed with³²P-labeled oligonucleotides at 30-36° C. overnight, washed in 2×SSC at30-36° C., and exposed to film.

For in vivo western blot analysis, tissue was dissected fromGFP-positive striatum, lysed in 150 μl of lysis buffer and protein levelquantified with the DC protein assay (Bio-Rad). 10 μg total protein wasseparated on an 8% SDS-polyacrylamide gel before transferring to a 0.45um PVDF membrane. The membrane was blocked with 2% milk in PBS-Tween 20(0.05%) and incubated with either an anti-huntingtin antibody (1:5000,Chemicon) or an anti-β-actin antibody (1:10,000, Sigma) followed by aconjugated goat anti-mouse secondary antibody (1:10,000, JacksonImmunoResearch) and ECL-Plus substrate (Amersham Biosciences) and thenexposed to film.

Immunohistochemical Analyses

Forty-micron thick, free-floating coronal brain sections were processedfor immunohistochemical visualization of striatal neurons (DARPP-32,1:100, Cell Signaling Technology) and microglia (Iba1, 1:1000, WAKO)using the biotin-labeled antibody procedure. Primary antibodyincubations were for 24 hours at room temperature. Sections wereincubated in goat anti-rabbit biotinylated IgG secondary antibodies(1:200, Vector Laboratories, 1 h at room temperature). In all stainingprocedures, deletion of the primary antibody served as a control.Sections were mounted onto Superfrost™ Plus slides and coverslipped withGelmount (Biomeda). Images were captured using an Olympus BX60 lightmicroscope and DP70 digital camera, along with Olympus DP Controllersoftware.

Statistical Analyses

All statistical analyses were performed using Sigma Stat statisticalsoftware. QPCR analyses for huntingtin and CD11b expression wereperformed using a one-way analysis of variance (ANOVA), as was northernblot densitometry analysis. Upon a significant effect, Bonferronipost-hoc analyses were performed to assess for significant differencesbetween individual groups. Western blot densitometry analysis wasperformed using a two-tailed Student's t-test. In all cases, P<0.05 wasconsidered significant.

Figure Preparation

All photographs were formatted with Adobe® Photoshop® software, allgraphs were made with Prism Graph software and all figures wereconstructed with Adobe® Illustrator software.

EXAMPLE 7 RNAi-Mediated Silencing of Genes

The inventors have previously shown that genes can be silenced in anallele-specific manner. They have also demonstrated that viral-mediateddelivery of siRNA can specifically reduce expression of targeted genesin various cell types, both in vitro and in vivo. This strategy was thenapplied to reduce expression of a neurotoxic polyglutamine diseaseprotein. The ability of viral vectors to transduce cells efficiently invivo, coupled with the efficacy of virally expressed siRNA shown here,extends the application of siRNA to viral-based therapies and in vivotargeting experiments that aim to define the function of specific genes.

Huntington's disease (HD) is one of several dominant neurodegenerativediseases that result from a similar toxic gain of function mutation inthe disease protein: expansion of a polyglutamine (polyQ)-encodingtract. It is well established that for HD and other polyglutaminediseases, the length of the expansion correlates inversely with age ofdisease onset. Animal models for HD have provided important clues as tohow mutant huntingtin (htt) induces pathogenesis. Currently, noneuroprotective treatment exists for HD. RNA interference has emerged asa leading candidate approach to reduce expression of disease genes bytargeting the encoding mRNA for degradation.

Although the effect of partial reduction of wildtype htt in adultneurons is unknown, it is advantageous to target only mutant htt fordegradation, if possible. Disease allele-specific RNAi are designedusing approaches that led to allele specific silencing for otherneurogenetic disease models. This allows directed silencing of themutant, disease-causing expanded allele, leaving the normal alleleintact.

Constitutive expression of shRNA can prevent the neuropathological andbehavioral phenotypes in a mouse model of Spinocerebellar Ataxia type I,a related polyQ disease. However, the constitutive expression of shRNAmay not be necessary, particularly for pathologies that take many yearsto develop but may be cleared in a few weeks or months. For this reason,and to reduce long-term effects that may arise if nonspecific silencingor activation of interferon responses is noted, controlled expressionmay be very important. In order to regulate RNAi for diseaseapplication, doxycycline-responsive vectors have been developed forcontrolled silencing in vitro.

Most eukaryotes encode a substantial number of small noncoding RNAstermed micro RNAs (miRNAs). mir-30 is a 22-nucleotide human miRNA thatcan be naturally processed from a longer transcript bearing the proposedmiR-30 stem-loop precursor. mir-30 can translationally inhibit anmRNA-bearing artificial target sites. The mir-30 precursor stem can besubstituted with a heterologous stem, which can be processed to yieldnovel miRNAs and can block the expression of endogenous mRNAs.

Two strategies are possible to target a particular sequence, such as thegene involved in Huntington's Disease (FIGS. 42A and 42B). One candevelop non-allele specific RNAi molecules, and candidates based on 8.2inhibitory RNAs have been developed. Alternatively, one can developallele-specific RNAi molecules. The inventors have worked to developRNAi molecules that target several key single nucleotide polymorphisms(SNPs). These RNAi molecules, however, may be limited to the treatmentof specific families/patients.

Another approach, which is the approach used in the present invention,the inventors targeted the expansion region. This approach has theadvantage of being able to treat entire HD populations, and not justthose with specific SNPs. These RNAi molecules are different becauseinstead of targeting a SNP for allele specificity, these sequences takeadvantage of structural integrity at the sites flanking the expansionregion. The siRNA data shows that they are effective. The presentinventors have also moved them into miRNA expression vectors, which werealso effective.

The inventors have generated and tested the following RNAi molecules:

siRNA Sequence HDAS 07 AUGAAGGCCUUCGAGUCCCUC (SEQ ID NO: 215) HDAS 18GGCGACCCUGGAAAAGCUGAU (SEQ ID NO: 216) HDAS 19 UGGCGACCCUGGAAAAGCUGA(SEQ ID NO: 217) HDAS 20 AUGGCGACCCUGGAAAAGCUG (SEQ ID NO: 218) SequencemiHD7A1 (SEQ ID NO: 219) AAAACUCGAGUGAGCGCUGAAGGCCUUCGAGUCCCUCA

UGAGGGACUCGAAGGCCUUCAU CGCCUACUAGUAAAA Sequence miHD7A2 (SEQ ID NO: 220)AAAACUCGAGUGAGCGCUGAAGGCCUUCGAGUCUUUUA

UGAGGGACUCGAAGGCCUUCAU CGCCUACUAGUAAAA Sequence miHD7B1 (SEQ ID NO: 221)AAAACUCGAGUGAGCGCAUGAAGGCCUUCGAGUCCCU

GAGGGACUCGAAGGCCUUCAUC CGCCUACUAGUAAAA Sequence miHD7B2 (SEQ ID NO: 222)AAAACUCGAGUGAGCGCAUGAAGGCCUUCGAGUCUUUU

GAGGGACUCGAAGGCCUUCAUC CGCCUACUAGUAAAA

The different fonts show the various parts of the miRNA. In sequentialorder, the stem sequence of the miRNA is shown in bold, then the sensestrand in regular type, then the loop sequence in bold italics, then theanti-sense strand in regular type, and last, part of stem sequence inbold.

The inventors generated constructs to assess allele-specific silencingof Htt (FIGS. 43A and 43B). Two plasmids were generated expressingfull-length wild type (FIG. 43A, pCMV-FLHtt 18Q-Flag) or mutanthuntingtin (FIG. 43B, pCMV-FLHtt 83Q-V5). Wild type and mutantfull-length huntingtin are expressed under the control of the CMVpromoter and each cDNA have distinct epitope tags to differentiate itsexpression by western blot. To normalize transfection efficiencieseither renilla (WT htt) or firefly (mutant htt) luciferase were includedon the same plasmid. This design allowed assessment of allelespecificity in the same cell after co-transfection.

Western blot and Q-PCR results indicate that the candidate siRNAs wereallele-specific in targeting mutant Htt, but not wild type Htt (FIGS.44A-44C). HEK293 cells were co-transfected with plasmids expressing wildtype and mutant huntingtin and with different siRNA sequence. Total RNAand protein lysates were obtained 24 hours after transfection. Afterscreening by Q-PCR and western blot, some of the siRNA design sequenceswere observed to preferentially silence the mutant allele. FIG. 44Ashows wild type Htt and FIG. 44B shows mutant Htt. As seen in FIG. 44C,siRNA sequence number 7 (S7) reduced mutant htt by 40% and the wild typehuntingtin by 6%.

The inventors found that formulated LNP siRNAs were distributed broadlyfollowing intrastriatal infusion, that formulated LNP siRNA reduced Httin adult mouse brain at biologically relevant dose, and siRNAs targetingsequences targeting the expansion provided for allele specificsilencing.

The inventors also found that miRNA shuttles for allele specificsilencing of htt could effectively be used (FIG. 45). miRNA shuttlesbased on the siRNA sequence 7 (S7) were generated. To assess silencespecificity, HEK293 cells were co-transfected with wild type and mutanthuntingtin plasmids and mi7A1, mi7A2, mi7B1, mi7B2 or miGFP as acontrol. Cells were harvested 24 hours after transfection and wild typeand mutant Htt silencing was determined by western blot. Mi7A 1 andmi7A2 had the most preferential silencing profile, the latter the mostbeneficial.

Sequence mi7A1 silences very efficiently either wild type or mutanthuntingtin. This is possibly due to an excess of mi7A1 production. Thespecificity of silencing of mi7A1 at high and low doses was compared.HEK293 cells were transfected with two different amounts of mi7A 1 andprotein lysates were obtained 24 hours after transfection. Silencing ofboth wild type and mutant huntingtin was determined by western blot withspecific antibodies against the epitope tags (FIGS. 46A and 46B). Datashows that preferential silencing for the mutant huntingtin is achievedwhen mi7A1 is transfected at a low dose. FIG. 46A shows normal Htt, andFIG. 46B shows mutant Htt.

The inventors also evaluated the strand biasing of miR shuttles (FIG.47). Different mutations were introduced to the 3′ end of the sensestrand of the mi7 sequences (mi7A2 and mi7B2) to promote antisensestrand loading into the RISC. To determine which strand waspreferentially loaded several luciferase reporter constructs based onpsicheck2 vector were designed. HEK293 cells were cotransfected withboth mi7 shuttle and a reporter construct for each strand and 24 hourslater cell extracts were obtained. Sequences 7A1 and 7A2 showedexceptional strand biasing.

All publications, patents and patent applications are incorporatedherein by reference. While in the foregoing specification this inventionhas been described in relation to certain preferred embodiments thereof,and many details have been set forth for purposes of illustration, itwill be apparent to those skilled in the art that the invention issusceptible to additional embodiments and that certain of the detailsdescribed herein may be varied considerably without departing from thebasic principles of the invention.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention are to be construed to cover boththe singular and the plural, unless otherwise indicated herein orclearly contradicted by context. The terms “comprising,” “having,”“including,” and “containing” are to be construed as open-ended terms(i.e., meaning “including, but not limited to”) unless otherwise noted.Recitation of ranges of values herein are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein, isintended merely to better illuminate the invention and does not pose alimitation on the scope of the invention unless otherwise claimed. Nolanguage in the specification should be construed as indicating anynon-claimed element as essential to the practice of the invention.

Embodiments of this invention are described herein, including the bestmode known to the inventors for carrying out the invention. Variationsof those embodiments may become apparent to those of ordinary skill inthe art upon reading the foregoing description. The inventors expectskilled artisans to employ such variations as appropriate, and theinventors intend for the invention to be practiced otherwise than asspecifically described herein. Accordingly, this invention includes allmodifications and equivalents of the subject matter recited in theclaims appended hereto as permitted by applicable law. Moreover, anycombination of the above-described elements in all possible variationsthereof is encompassed by the invention unless otherwise indicatedherein or otherwise clearly contradicted by context.

1. A nucleic acid encoding an artificial primary miRNA transcript(pri-miRNA) consisting of, in order of position, a 5′-flanking region, afirst siRNA region, a loop region, a second siRNA region, and a3′-flanking region.
 2. The nucleic acid of claim 1, wherein the5′-flanking region is contiguously linked to the first siRNA region, theloop region is positioned between the first siRNA region and the secondsiRNA region, and the second siRNA region is contiguously linked to the3′-flanking region.
 3. The nucleic acid of claim 1, wherein the firstsiRNA region is a non-guide region and the second siRNA region is aguide region.
 4. The nucleic acid of claim 1, wherein the first siRNAregion is a guide region and the second siRNA region is a non-guideregion.
 5. The nucleic acid of claim 1, wherein the 5′-flanking regioncomprises a 5′-joining sequence contiguously linked to the first siRNAregion.
 6. The nucleic acid of claim 5, wherein the 5′-joining sequenceconsists of 5-7 nucleotides.
 7. The nucleic acid of claim 6, wherein the5′-joining sequence consists of 6 nucleotides.
 8. The nucleic acid ofclaim 5, wherein the 5′-joining sequence encodes GUGASSS, wherein S iseither a G or C nucleotide.
 9. The nucleic acid of claim 5, wherein the5′-joining sequence encodes GUGAGCG.
 10. The nucleic acid of claim 1,wherein the 5′-flanking region further comprises a 5′-bulge sequencepositioned upstream from the 5′-joining sequence.
 11. The nucleic acidof claim 10, wherein the 5′-bulge sequence comprises a cloning site. 12.The nucleic acid of claim 11, wherein cloning site encodes an XhoI site.13. The nucleic acid of claim 10, wherein the 5′-bulge sequence consistsof about 1-10 nucleotides.
 14. The nucleic acid of claim 10, wherein the5′-bulge sequence encodes UAAACUCGA.
 15. The nucleic acid of claim 1,wherein the 5′-flanking region further comprises a 5′-spacer sequencepositioned upstream from the 5′-bulge sequence.
 16. The nucleic acid ofclaim 15, wherein the 5′-spacer sequence consists of 10-12 nucleotides.17. The nucleic acid of claim 15, wherein the 5′-spacer sequence isUGGUACCGUU (SEQ ID NO: 180).
 18. The nucleic acid of any one of claims15-17, wherein the 5′-flanking region further comprising a 5′-upstreamsequence positioned upstream from the 5′-spacer sequence.
 19. Thenucleic acid of claim 18, wherein the 5′-upstream sequence is about30-2000 nucleotides in length.
 20. The nucleic acid of claim 1, whereinthe 3′-flanking region comprises a 3′-joining sequence contiguouslylinked to the second siRNA region.
 21. The nucleic acid of claim 20,wherein the 3′-joining sequence consists of 5-7 nucleotides.
 22. Thenucleic acid of claim 20, wherein the 3′-joining sequence is at leastabout 85% complementary to the 5′-joining sequence.
 23. The nucleic acidof claim 20, wherein the 3′-joining sequence encodes CGCYUAC, wherein Yis C or U.
 24. The nucleic acid of claim 20, wherein the 3′-joiningsequence encodes CGCCUAC.
 25. The nucleic acid of any one of claims20-24, wherein the 3′-flanking region further comprises a 3′-bulgesequence positioned downstream from the 3′-joining sequence.
 26. Thenucleic acid of claim 25, wherein the 3′-bulge sequence comprises acloning site.
 27. The nucleic acid of claim 26, wherein cloning siteencodes a SpeI/XbaI site or a SpeI site.
 28. The nucleic acid of claim25, wherein the 3′-bulge sequence consists of about 1-10 nucleotides.29. The nucleic acid of claim 25, wherein 3′-bulge sequence encodes UAG.30. The nucleic acid of claim 25, wherein the 5′-bulge sequence iscomplementary to the 3′-bulge sequence at only one nucleotide at eachend of the bulge sequence.
 31. The nucleic acid of claim 1, wherein the3′-flanking region further comprises a 3′-spacer sequence positioneddownstream from the 3′-bulge sequence.
 32. The nucleic acid of claim 31,wherein the 3′-spacer sequence consists of 10-12 nucleotides.
 33. Thenucleic acid of claim 31, wherein the 3′-spacer sequence is AGCGGCCGCCA(SEQ ID NO: 181).
 34. The nucleic acid of claim 1, wherein the 3′-spacersequence is at least about 70% complementary to the 5′-spacer sequence.35. The nucleic acid of claim 1, wherein the 3′-flanking region furthercomprises a 3′-downstream sequence positioned downstream from the3′-spacer sequence.
 36. The nucleic acid of claim 35, wherein the5′-upstream sequence does not significantly pair with the 3′-downstreamsequence.
 37. The nucleic acid of claim 35 or 36, wherein the3′-downstream sequence is about 30-2000 nucleotides in length.
 38. Thenucleic acid of claim 1, wherein the loop region is from 15-19nucleotides in length.
 39. The nucleic acid of claim 38, wherein theloop region is 17 nucleotides in length.
 40. The nucleic acid of claim1, wherein the loop region encodes CUNNNNNNNNNNNNNNNGG or (SEQ ID NO:182) or CCNNNNNNNNNNNNNNNGG (SEQ ID NO: 183).
 41. The nucleic acid ofclaim 1, wherein the loop region encodes CUGUGAAGCCACAGAUGGG or (SEQ IDNO: 184) or CCGUGAAGCCACAGAUGGG (SEQ ID NO: 185)
 42. The nucleic acid ofclaim 1, which nucleic acid does not encode a sequence consisting of SEQID NO:219, SEQ ID NO:220, SEQ ID NO:221 or SEQ ID NO:222.
 43. An RNAencoded by nucleic acid of any one of claims 1-42.
 44. An expressioncassette comprising a promoter contiguously linked to the nucleic acidof claim
 1. 45-78. (canceled)